9PDR | pdb_00009pdr

Composite map of PIC-Med-SWI/SNF-Nucleosome

PDB DOI: https://doi.org/10.2210/pdb9PDR/pdb
EM Map EMD-71541: EMDB EMDataResource

Classification: TRANSCRIPTION/DNA
Organism(s): Saccharomyces cerevisiae, Xenopus laevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-07-01 Released: 2026-10-14
Deposition Author(s): Yang, C., Nagai, S., Chen, D.-H.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Composite map of PIC-Med-SWI/SNF-Nucleosome

Yang, C., Nagai, S., Chen, D.-H.

To be published.

Macromolecule Content

Total Structure Weight: 8,553.74 kDa
Atom Count: 341,540
Modeled Residue Count: 40,942
Deposited Residue Count: 73,958
Unique protein chains: 66
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPD/RAD3	A [auth A0], GC [auth B0]	778	Saccharomyces cerevisiae	Mutation(s): 0 EC: 5.6.2.3
UniProt
Find proteins for P06839 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06839 Go to UniProtKB: P06839
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UniProt Group	P06839
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB1	B [auth A1], HC [auth B1]	642	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32776 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32776 Go to UniProtKB: P32776
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UniProt Group	P32776
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB2	C [auth A2], IC [auth B2]	513	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02939 Go to UniProtKB: Q02939
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UniProt Group	Q02939
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II transcription factor B subunit 3	D [auth A3], JC [auth B3]	321	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q03290 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03290 Go to UniProtKB: Q03290
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UniProt Group	Q03290
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB4	E [auth A4], KC [auth B4]	338	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12004 Go to UniProtKB: Q12004
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UniProt Group	Q12004
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit TFB5	F [auth A5], LC [auth B5]	72	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7C1 Go to UniProtKB: Q3E7C1
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UniProt Group	Q3E7C1
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH subunit SSL1	G [auth A6], MC [auth B6]	461	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04673 Go to UniProtKB: Q04673
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UniProt Group	Q04673
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPB	H [auth A7], NC [auth B7]	843	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q00578 Go to UniProtKB: Q00578
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UniProt Group	Q00578
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SNF5	EE [auth nF] I [auth A8] NB [auth SF] OC [auth B8] TE [auth sF] EE [auth nF], I [auth A8], NB [auth SF], OC [auth B8], TE [auth sF], YA [auth NF]	905	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P18480 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18480 Go to UniProtKB: P18480
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18480
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14	J [auth A9], PC [auth B9]	244	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35189 Go to UniProtKB: P35189
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UniProt Group	P35189
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	HA [auth MA], K [auth AA], ND [auth mA], QC [auth BA]	1,733	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
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UniProt Group	P04050
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	L [auth AB], RC [auth BB]	1,224	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
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UniProt Group	P08518
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	M [auth AC], SC [auth BC]	318	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
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UniProt Group	P16370
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	N [auth AD], TC [auth BD]	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433 Go to UniProtKB: P20433
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UniProt Group	P20433
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	O [auth AE], UC [auth BE]	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
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UniProt Group	P20434
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	P [auth AF], VC [auth BF]	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
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UniProt Group	P20435
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	Q [auth AG], WC [auth BG]	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087 Go to UniProtKB: P34087
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UniProt Group	P34087
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	R [auth AH], XC [auth BH]	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
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UniProt Group	P20436
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	S [auth AI], YC [auth BI]	122	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
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UniProt Group	P27999
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	T [auth AJ], ZC [auth BJ]	70	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB10, YOR210W
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
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UniProt Group	P22139
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	AD [auth BK], U [auth AK]	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
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UniProt Group	P38902
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	BD [auth BL], V [auth AL]	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
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UniProt Group	P40422
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIB	CD [auth BM], W [auth AM]	345	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SUA7, YPR086W, P9513.4
UniProt
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29055 Go to UniProtKB: P29055
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UniProt Group	P29055
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box-binding protein	ED [auth BO], Y [auth AO]	240	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SPT15, BTF1, TBP1, YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P13393 Go to UniProtKB: P13393
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UniProt Group	P13393
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit alpha	FD [auth BQ], Z [auth AQ]	735	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41895 Go to UniProtKB: P41895
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UniProt Group	P41895
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIF subunit beta	AA [auth AR], GD [auth BR]	400	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41896 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41896 Go to UniProtKB: P41896
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UniProt Group	P41896
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor S-II	BA [auth AS], HD [auth BS]	309	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DST1, PPR2, YGL043W
UniProt
Find proteins for P07273 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07273 Go to UniProtKB: P07273
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UniProt Group	P07273
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA large subunit	DA [auth AU], JD [auth BU]	286	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TOA1, YOR194C
UniProt
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32773 Go to UniProtKB: P32773
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UniProt Group	P32773
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIA subunit 2	EA [auth AV], KD [auth BV]	122	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TOA2, YKL058W
UniProt
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32774 Go to UniProtKB: P32774
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UniProt Group	P32774
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit alpha	FA [auth AW], LD [auth BW]	482	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36100 Go to UniProtKB: P36100
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UniProt Group	P36100
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor IIE subunit beta	GA [auth AX], MD [auth BX]	328	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36145 Go to UniProtKB: P36145
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UniProt Group	P36145
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 6	IA [auth Ma], OD [auth ma]	295	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38782 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38782 Go to UniProtKB: P38782
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UniProt Group	P38782
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 8	JA [auth Mb], PD [auth mb]	223	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38304 Go to UniProtKB: P38304
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UniProt Group	P38304
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 11	KA [auth Mc], QD [auth mc]	115	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99278 Go to UniProtKB: Q99278
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UniProt Group	Q99278
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 17	LA [auth Md], RD [auth md]	687	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32569 Go to UniProtKB: P32569
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UniProt Group	P32569
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 18	MA [auth Me], SD [auth me]	307	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32585 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32585 Go to UniProtKB: P32585
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UniProt Group	P32585
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 20	NA [auth Mf], TD [auth mf]	210	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34162 Go to UniProtKB: P34162
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UniProt Group	P34162
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 22	OA [auth Mg], UD [auth mg]	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32570 Go to UniProtKB: P32570
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UniProt Group	P32570
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 4	PA [auth Mh], VD [auth mh]	284	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12343 Go to UniProtKB: Q12343
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UniProt Group	Q12343
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 7	QA [auth Mi], WD [auth mi]	222	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q08278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08278 Go to UniProtKB: Q08278
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UniProt Group	Q08278
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 9	RA [auth Mj], XD [auth mj]	149	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P33308 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33308 Go to UniProtKB: P33308
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UniProt Group	P33308
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 10	SA [auth Mk], YD [auth mk]	157	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q06213 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06213 Go to UniProtKB: Q06213
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UniProt Group	Q06213
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 14	DC [auth t4], TA [auth Ml], XB [auth T4], ZD [auth ml]	1,082	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P19263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19263 Go to UniProtKB: P19263
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UniProt Group	P19263
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 19	AE [auth mm], UA [auth Mm]	220	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25046 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25046 Go to UniProtKB: P25046
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UniProt Group	P25046
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 21	BE [auth mn], VA [auth Mn]	140	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P47822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47822 Go to UniProtKB: P47822
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UniProt Group	P47822
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 31	CE [auth mo], WA [auth Mo]	127	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38633 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38633 Go to UniProtKB: P38633
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UniProt Group	P38633
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1	DE [auth mp], XA [auth Mp]	566	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12321 Go to UniProtKB: Q12321
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UniProt Group	Q12321
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF2	FE [auth nP], PB [auth SH], VE [auth sH], ZA [auth NP]	1,703	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P22082 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22082 Go to UniProtKB: P22082
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UniProt Group	P22082
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	AB [auth No], EB [auth Ns], GE [auth no], KE [auth ns]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
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UniProt Group	P84233
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	BB [auth Np], FB [auth Nt], HE [auth np], LE [auth nt]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62798 (Xenopus borealis) Explore P62798 Go to UniProtKB: P62798
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UniProt Group	P62798
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	CB [auth Nq], GB [auth Nu], IE [auth nq], ME [auth nu]	130	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
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UniProt Group	P06897
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	DB [auth Nr], HB [auth Nv], JE [auth nr], NE [auth nv]	126	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
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UniProt Group	P02281
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF12	IB [auth SA], OE [auth sA]	566	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53628 Go to UniProtKB: P53628
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UniProt Group	P53628
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF complex subunit SWI3	JB [auth SB], LB [auth SD], PE [auth sB], RE [auth sD]	825	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32591 Go to UniProtKB: P32591
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UniProt Group	P32591
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulatory protein SNF6	KB [auth SC], QE [auth sC]	332	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P18888 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P18888 Go to UniProtKB: P18888
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UniProt Group	P18888
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF global transcription activator complex subunit SWP82	MB [auth SE], SE [auth sE]	623	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P43554 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43554 Go to UniProtKB: P43554
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UniProt Group	P43554
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
unsigned peptide of SWI/SNF	OB [auth SG], UE [auth sG]	47	Saccharomyces cerevisiae	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
SWI/SNF chromatin-remodeling complex subunit SWI1	QB [auth SI], WE [auth sI]	1,314	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P09547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09547 Go to UniProtKB: P09547
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UniProt Group	P09547
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of Ty1 transposition protein 102	RB [auth SJ], XE [auth sJ]	157	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53330 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53330 Go to UniProtKB: P53330
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UniProt Group	P53330
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 7	SB [auth SK], YE [auth sK]	477	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12406 Go to UniProtKB: Q12406
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UniProt Group	Q12406
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein ARP9	TB [auth SL], ZE [auth sL]	467	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q05123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05123 Go to UniProtKB: Q05123
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UniProt Group	Q05123
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 2	AC [auth t1], UB [auth T1]	431	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12124 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12124 Go to UniProtKB: Q12124
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UniProt Group	Q12124
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 3	BC [auth t2], VB [auth T2]	397	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40356 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40356 Go to UniProtKB: P40356
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UniProt Group	P40356
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 5	CC [auth t3], WB [auth T3]	1,132	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53114 Go to UniProtKB: P53114
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UniProt Group	P53114
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 15	EC [auth t5], YB [auth T5]	1,081	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P19659 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19659 Go to UniProtKB: P19659
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UniProt Group	P19659
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 16	FC [auth t6], ZB [auth T6]	974	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32259 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32259 Go to UniProtKB: P32259
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UniProt Group	P32259
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Molecule	Chains	Length	Organism
Entity ID: 24
promoter DNA	DD [auth BN], X [auth AN]	238	Saccharomyces cerevisiae
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Molecule	Chains	Length	Organism
Entity ID: 29
promoter DNA	CA [auth AT], ID [auth BT]	238	Saccharomyces cerevisiae
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain UF [auth B0] SDF format, chain AF [auth A0] MOL2 format, chain UF [auth B0] MOL2 format, chain AF [auth A0] mmCIF format, chain UF [auth B0] mmCIF format, chain AF [auth A0]	AF [auth A0], UF [auth B0]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AF [auth A0] Focus chain UF [auth B0] Interactions & Density Focus chain AF [auth A0] Focus chain UF [auth B0]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AG [auth B6] SDF format, chain DF [auth A4] SDF format, chain EF [auth A6] SDF format, chain FF [auth A6] SDF format, chain GG [auth BC] SDF format, chain HG [auth BI] SDF format, chain JG [auth BJ] SDF format, chain KG [auth BL] SDF format, chain LF [auth AB] SDF format, chain LG [auth BM] SDF format, chain MF [auth AC] SDF format, chain OF [auth AI] SDF format, chain PF [auth AJ] SDF format, chain SF [auth AS] SDF format, chain VF [auth B3] SDF format, chain XF [auth B4] SDF format, chain ZF [auth B6] SDF format, chain YF [auth B6] SDF format, chain WF [auth B3] SDF format, chain TF [auth AW] SDF format, chain RF [auth AM] SDF format, chain QF [auth AL] SDF format, chain NG [auth BW] SDF format, chain NF [auth AI] SDF format, chain MG [auth BS] SDF format, chain JF [auth AA] SDF format, chain IG [auth BI] SDF format, chain IF [auth AA] SDF format, chain HF [auth A6] SDF format, chain GF [auth A6] SDF format, chain FG [auth BB] SDF format, chain DG [auth BA] SDF format, chain CG [auth BA] SDF format, chain CF [auth A3] SDF format, chain BG [auth B6] SDF format, chain BF [auth A3] MOL2 format, chain AG [auth B6] MOL2 format, chain DF [auth A4] MOL2 format, chain EF [auth A6] MOL2 format, chain FF [auth A6] MOL2 format, chain GG [auth BC] MOL2 format, chain HG [auth BI] MOL2 format, chain JG [auth BJ] MOL2 format, chain KG [auth BL] MOL2 format, chain LF [auth AB] MOL2 format, chain LG [auth BM] MOL2 format, chain MF [auth AC] MOL2 format, chain OF [auth AI] MOL2 format, chain PF [auth AJ] MOL2 format, chain SF [auth AS] MOL2 format, chain VF [auth B3] MOL2 format, chain XF [auth B4] MOL2 format, chain ZF [auth B6] MOL2 format, chain YF [auth B6] MOL2 format, chain WF [auth B3] MOL2 format, chain TF [auth AW] MOL2 format, chain RF [auth AM] MOL2 format, chain QF [auth AL] MOL2 format, chain NG [auth BW] MOL2 format, chain NF [auth AI] MOL2 format, chain MG [auth BS] MOL2 format, chain JF [auth AA] MOL2 format, chain IG [auth BI] MOL2 format, chain IF [auth AA] MOL2 format, chain HF [auth A6] MOL2 format, chain GF [auth A6] MOL2 format, chain FG [auth BB] MOL2 format, chain DG [auth BA] MOL2 format, chain CG [auth BA] MOL2 format, chain CF [auth A3] MOL2 format, chain BG [auth B6] MOL2 format, chain BF [auth A3] mmCIF format, chain AG [auth B6] mmCIF format, chain DF [auth A4] mmCIF format, chain EF [auth A6] mmCIF format, chain FF [auth A6] mmCIF format, chain GG [auth BC] mmCIF format, chain HG [auth BI] mmCIF format, chain JG [auth BJ] mmCIF format, chain KG [auth BL] mmCIF format, chain LF [auth AB] mmCIF format, chain LG [auth BM] mmCIF format, chain MF [auth AC] mmCIF format, chain OF [auth AI] mmCIF format, chain PF [auth AJ] mmCIF format, chain SF [auth AS] mmCIF format, chain VF [auth B3] mmCIF format, chain XF [auth B4] mmCIF format, chain ZF [auth B6] mmCIF format, chain YF [auth B6] mmCIF format, chain WF [auth B3] mmCIF format, chain TF [auth AW] mmCIF format, chain RF [auth AM] mmCIF format, chain QF [auth AL] mmCIF format, chain NG [auth BW] mmCIF format, chain NF [auth AI] mmCIF format, chain MG [auth BS] mmCIF format, chain JF [auth AA] mmCIF format, chain IG [auth BI] mmCIF format, chain IF [auth AA] mmCIF format, chain HF [auth A6] mmCIF format, chain GF [auth A6] mmCIF format, chain FG [auth BB] mmCIF format, chain DG [auth BA] mmCIF format, chain CG [auth BA] mmCIF format, chain CF [auth A3] mmCIF format, chain BG [auth B6] mmCIF format, chain BF [auth A3]	AG [auth B6] BF [auth A3] BG [auth B6] CF [auth A3] CG [auth BA] AG [auth B6], BF [auth A3], BG [auth B6], CF [auth A3], CG [auth BA], DF [auth A4], DG [auth BA], EF [auth A6], FF [auth A6], FG [auth BB], GF [auth A6], GG [auth BC], HF [auth A6], HG [auth BI], IF [auth AA], IG [auth BI], JF [auth AA], JG [auth BJ], KG [auth BL], LF [auth AB], LG [auth BM], MF [auth AC], MG [auth BS], NF [auth AI], NG [auth BW], OF [auth AI], PF [auth AJ], QF [auth AL], RF [auth AM], SF [auth AS], TF [auth AW], VF [auth B3], WF [auth B3], XF [auth B4], YF [auth B6], ZF [auth B6]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AG [auth B6] Focus chain BF [auth A3] Focus chain BG [auth B6] Focus chain CF [auth A3] Focus chain CG [auth BA] Focus chain DF [auth A4] Focus chain DG [auth BA] Focus chain EF [auth A6] Focus chain FF [auth A6] Focus chain FG [auth BB] Focus chain GF [auth A6] Focus chain GG [auth BC] Focus chain HF [auth A6] Focus chain HG [auth BI] Focus chain IF [auth AA] Focus chain IG [auth BI] Focus chain JF [auth AA] Focus chain JG [auth BJ] Focus chain KG [auth BL] Focus chain LF [auth AB] Focus chain LG [auth BM] Focus chain MF [auth AC] Focus chain MG [auth BS] Focus chain NF [auth AI] Focus chain NG [auth BW] Focus chain OF [auth AI] Focus chain PF [auth AJ] Focus chain QF [auth AL] Focus chain RF [auth AM] Focus chain SF [auth AS] Focus chain TF [auth AW] Focus chain VF [auth B3] Focus chain WF [auth B3] Focus chain XF [auth B4] Focus chain YF [auth B6] Focus chain ZF [auth B6] Interactions & Density Focus chain AG [auth B6] Focus chain BF [auth A3] Focus chain BG [auth B6] Focus chain CF [auth A3] Focus chain CG [auth BA] Focus chain DF [auth A4] Focus chain DG [auth BA] Focus chain EF [auth A6] Focus chain FF [auth A6] Focus chain FG [auth BB] Focus chain GF [auth A6] Focus chain GG [auth BC] Focus chain HF [auth A6] Focus chain HG [auth BI] Focus chain IF [auth AA] Focus chain IG [auth BI] Focus chain JF [auth AA] Focus chain JG [auth BJ] Focus chain KG [auth BL] Focus chain LF [auth AB] Focus chain LG [auth BM] Focus chain MF [auth AC] Focus chain MG [auth BS] Focus chain NF [auth AI] Focus chain NG [auth BW] Focus chain OF [auth AI] Focus chain PF [auth AJ] Focus chain QF [auth AL] Focus chain RF [auth AM] Focus chain SF [auth AS] Focus chain TF [auth AW] Focus chain VF [auth B3] Focus chain WF [auth B3] Focus chain XF [auth B4] Focus chain YF [auth B6] Focus chain ZF [auth B6]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain KF [auth AA] SDF format, chain EG [auth BA] MOL2 format, chain KF [auth AA] MOL2 format, chain EG [auth BA] mmCIF format, chain KF [auth AA] mmCIF format, chain EG [auth BA]	EG [auth BA], KF [auth AA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EG [auth BA] Focus chain KF [auth AA] Interactions & Density Focus chain EG [auth BA] Focus chain KF [auth AA]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK Query on UNK	OB [auth SG], UE [auth sG]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Yang, C.

Nagai, S.

Chen, D.-H.

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release

9PDR | pdb_00009pdr

Composite map of PIC-Med-SWI/SNF-Nucleosome

Literature

Composite map of PIC-Med-SWI/SNF-Nucleosome

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt