7D4I

Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F)

PDB DOI: https://doi.org/10.2210/pdb7D4I/pdb
NAKB: 7D4I
EM Map EMD-30574: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): Yes

Deposited: 2020-09-24 Released: 2021-10-06
Deposition Author(s): Du, Y., Zhang, J., An, W., Ye, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1

Ye, K.

To be published.

Macromolecule Content

Total Structure Weight: 5,300.1 kDa
Atom Count: 253,642
Modelled Residue Count: 30,658
Deposited Residue Count: 41,852
Unique protein chains: 76
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S1-A	D [auth SC]	255	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33442 Go to UniProtKB: P33442
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UniProt Group	P33442
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4-A	E [auth SF]	261	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX35 Go to UniProtKB: P0CX35
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UniProt Group	P0CX35
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	F [auth SG]	225	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26783 Go to UniProtKB: P26783
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UniProt Group	P26783
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6-A	G [auth SH]	236	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX37 Go to UniProtKB: P0CX37
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UniProt Group	P0CX37
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7-A	H [auth SI]	190	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26786 Go to UniProtKB: P26786
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UniProt Group	P26786
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8-A	I [auth SJ]	200	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX39 Go to UniProtKB: P0CX39
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CX39
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9-A	J [auth SK]	197	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O13516 Go to UniProtKB: O13516
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UniProt Group	O13516
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11-A	K [auth SM]	156	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX47 Go to UniProtKB: P0CX47
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UniProt Group	P0CX47
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	L [auth SO]	151	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05756 Go to UniProtKB: P05756
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UniProt Group	P05756
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14-A	M [auth SP]	137	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06367 Go to UniProtKB: P06367
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UniProt Group	P06367
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16-A	N [auth SR]	143	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX51 Go to UniProtKB: P0CX51
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CX51
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18-A	O [auth ST]	146	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX55 Go to UniProtKB: P0CX55
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UniProt Group	P0CX55
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19-A	P [auth SU]	144	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07280 Go to UniProtKB: P07280
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UniProt Group	P07280
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S22-B	Q [auth SX]	130	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E7Y3 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7Y3 Go to UniProtKB: Q3E7Y3
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3E7Y3
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23-A	R [auth SY]	145	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX29 Go to UniProtKB: P0CX29
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UniProt Group	P0CX29
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24-A	S [auth SZ]	135	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX31 Go to UniProtKB: P0CX31
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CX31
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27-A	T [auth Sc]	82	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35997 Go to UniProtKB: P35997
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UniProt Group	P35997
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28-A	U [auth Sd]	67	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7X9 Go to UniProtKB: Q3E7X9
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UniProt Group	Q3E7X9
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA 2'-O-methyltransferase fibrillarin	V [auth 3B], W [auth 3C]	327	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.1.1
UniProt
Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15646 Go to UniProtKB: P15646
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UniProt Group	P15646
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 56	X [auth 3D]	504	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12460 Go to UniProtKB: Q12460
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UniProt Group	Q12460
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar protein 58	Y [auth 3E]	511	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12499 Go to UniProtKB: Q12499
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12499
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA-processing protein 9	Z [auth 3F]	573	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06506 Go to UniProtKB: Q06506
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06506
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
13 kDa ribonucleoprotein-associated protein	AA [auth 3G], BA [auth 3H]	126	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39990 Go to UniProtKB: P39990
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UniProt Group	P39990
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 4	CA [auth A4]	776	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06679 Go to UniProtKB: Q06679
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UniProt Group	Q06679
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 5	DA [auth A5]	643	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q04177 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04177 Go to UniProtKB: Q04177
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UniProt Group	Q04177
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 8	EA [auth A8]	713	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53276 Go to UniProtKB: P53276
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UniProt Group	P53276
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 9	FA [auth A9]	575	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38882 Go to UniProtKB: P38882
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UniProt Group	P38882
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 10	GA [auth AE]	1,769	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P42945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P42945 Go to UniProtKB: P42945
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UniProt Group	P42945
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 15	HA [auth AF]	513	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q04305 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04305 Go to UniProtKB: Q04305
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UniProt Group	Q04305
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NET1-associated nuclear protein 1	IA [auth AG]	896	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02931 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02931 Go to UniProtKB: Q02931
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UniProt Group	Q02931
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Periodic tryptophan protein 2	JA [auth B1]	900	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25635 Go to UniProtKB: P25635
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UniProt Group	P25635
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 12	KA [auth B2]	943	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12220 Go to UniProtKB: Q12220
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UniProt Group	Q12220
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 13	LA [auth B3]	817	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05946 Go to UniProtKB: Q05946
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UniProt Group	Q05946
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 18	MA [auth B8]	594	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40362 Go to UniProtKB: P40362
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UniProt Group	P40362
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 21	NA [auth BE]	939	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06078 Go to UniProtKB: Q06078
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UniProt Group	Q06078
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 6	OA [auth B6]	440	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02354 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02354 Go to UniProtKB: Q02354
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UniProt Group	Q02354
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Bud site selection protein 21	PA [auth 5B]	214	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08492 Go to UniProtKB: Q08492
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UniProt Group	Q08492
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 7	QA [auth 5C]	554	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40055 Go to UniProtKB: P40055
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UniProt Group	P40055
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 11	RA [auth 5D]	250	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P34247 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34247 Go to UniProtKB: P34247
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UniProt Group	P34247
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein MPP10	SA [auth 5E]	593	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47083 Go to UniProtKB: P47083
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UniProt Group	P47083
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar ribonucleoprotein protein IMP3	TA [auth 5F]	183	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P32899 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32899 Go to UniProtKB: P32899
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UniProt Group	P32899
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar ribonucleoprotein protein IMP4	UA [auth 5G]	290	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53941 Go to UniProtKB: P53941
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UniProt Group	P53941
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Something about silencing protein 10	VA [auth 5H]	610	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12136 Go to UniProtKB: Q12136
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UniProt Group	Q12136
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SOF1	WA [auth 5I]	489	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P33750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33750 Go to UniProtKB: P33750
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UniProt Group	P33750
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein FCF2	XA [auth 5J]	217	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12035 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12035 Go to UniProtKB: Q12035
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UniProt Group	Q12035
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA-processing protein FCF1	YA [auth 5K]	189	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05498 Go to UniProtKB: Q05498
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UniProt Group	Q05498
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA biogenesis protein RRP5	ZA [auth RD]	1,729	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05022 Go to UniProtKB: Q05022
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UniProt Group	Q05022
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 22	AB [auth RE]	1,237	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53254 Go to UniProtKB: P53254
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA-processing protein 7	BB [auth RF]	297	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25368 Go to UniProtKB: P25368
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UniProt Group	P25368
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA small subunit methyltransferase NEP1	CB [auth RG], DB [auth RH]	252	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.1.1.260
UniProt
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06287 Go to UniProtKB: Q06287
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UniProt Group	Q06287
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome biogenesis protein BMS1	EB [auth RJ]	1,183	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08965 Go to UniProtKB: Q08965
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UniProt Group	Q08965
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA 3'-terminal phosphate cyclase-like protein	FB [auth RK]	367	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08096 Go to UniProtKB: Q08096
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UniProt Group	Q08096
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar complex protein 14	GB [auth RN]	810	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q99207 Go to UniProtKB: Q99207
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleolar complex protein 4	HB [auth RO]	552	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q06512 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06512 Go to UniProtKB: Q06512
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UniProt Group	Q06512
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 20	IB [auth RP]	2,493	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35194 Go to UniProtKB: P35194
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UniProt Group	P35194
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-associated protein 14	JB [auth RQ]	899	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q04500 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04500 Go to UniProtKB: Q04500
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UniProt Group	Q04500
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
Essential nuclear protein 1	KB [auth RS]	480	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38333 Go to UniProtKB: P38333
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UniProt Group	P38333
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
Pno1	LB [auth RT]	326	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of rDNA transcription protein 14	MB [auth RW]	206	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40470 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40470 Go to UniProtKB: P40470
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UniProt Group	P40470
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DHR1	NB [auth RZ]	1,267	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for Q04217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04217 Go to UniProtKB: Q04217
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UniProt Group	Q04217
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned peptides 1	OB [auth X1]	611	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Unassigned peptides 2	PB [auth X2]	694	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP45	QB [auth R5]	305	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05636 Go to UniProtKB: Q05636
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UniProt Group	Q05636
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component SKI6	RB [auth R1]	246	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46948 Go to UniProtKB: P46948
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UniProt Group	P46948
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP43	SB [auth R3]	394	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25359 Go to UniProtKB: P25359
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP46	TB [auth R6]	223	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53256 Go to UniProtKB: P53256
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UniProt Group	P53256
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP42	UB [auth R2]	265	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12277 Go to UniProtKB: Q12277
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UniProt Group	Q12277
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component MTR3	VB [auth M3]	250	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48240 Go to UniProtKB: P48240
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP40	WB [auth R0]	240	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08285 Go to UniProtKB: Q08285
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UniProt Group	Q08285
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Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component RRP4	XB [auth r4]	359	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38792 Go to UniProtKB: P38792
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UniProt Group	P38792
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Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex component CSL4	YB [auth C4]	292	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53859 Go to UniProtKB: P53859
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UniProt Group	P53859
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Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex exonuclease DIS3	ZB [auth R4]	1,001	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08162 Go to UniProtKB: Q08162
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UniProt Group	Q08162
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Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex exonuclease RRP6	AC [auth r6]	733	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12149 Go to UniProtKB: Q12149
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UniProt Group	Q12149
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
Exosome complex protein LRP1	BC [auth R7]	184	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38801 Go to UniProtKB: P38801
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UniProt Group	P38801
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Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DOB1	CC [auth M4]	1,073	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.6.4.13
UniProt
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47047 Go to UniProtKB: P47047
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UniProt Group	P47047
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Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
M-phase phosphoprotein 6 homolog	DC [auth M6]	186	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P53725 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53725 Go to UniProtKB: P53725
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UniProt Group	P53725
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Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain GC [auth RJ] MOL2 format, chain GC [auth RJ] mmCIF format, chain GC [auth RJ]	GC [auth RJ]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain GC [auth RJ] Interactions & Density Focus chain GC [auth RJ]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain IC [auth RZ] MOL2 format, chain IC [auth RZ] mmCIF format, chain IC [auth RZ]	IC [auth RZ]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain IC [auth RZ] Interactions & Density Focus chain IC [auth RZ]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EC [auth Sc] SDF format, chain FC [auth 5K] MOL2 format, chain EC [auth Sc] MOL2 format, chain FC [auth 5K] mmCIF format, chain EC [auth Sc] mmCIF format, chain FC [auth 5K]	EC [auth Sc], FC [auth 5K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EC [auth Sc] Focus chain FC [auth 5K] Interactions & Density Focus chain EC [auth Sc] Focus chain FC [auth 5K]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain HC [auth RJ] MOL2 format, chain HC [auth RJ] mmCIF format, chain HC [auth RJ]	HC [auth RJ]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HC [auth RJ] Interactions & Density Focus chain HC [auth RJ]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91940302, 91540201, 31430024, 31325007
Chinese Academy of Sciences	China	XDB08010203

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Entity ID: 1
Molecule	Chains	Length	Organism	Image
U3 snoRNA	A [auth 3A]	333	Saccharomyces cerevisiae S288C
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Validate Data

Deposit Data

Help and Resources

7D4I

Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F)

Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1

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