9A88 | pdb_00009a88

Structure of the pre-incision complex in nucleotide excision repair

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb9A88/pdb
NAKB: 9A88

Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-03-11 Released: 2024-10-09
Deposition Author(s): Yu, J., Yan, C.Y., Paul, T., Brewer, L., Tsutakawa, S.E., Tsai, C.-L., Hamdan, S., Tainer, J.A., Ivanov, I.

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

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

Literature

Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

Yu, J., Yan, C., Paul, T., Brewer, L., Tsutakawa, S.E., Tsai,C.-L., Hamdan, S.M., Tainer, J.A., Ivanov, I.

(2024) Nat Commun

DOI: https://doi.org/10.1038/s41467-024-52860-y

Macromolecule Content

Total Structure Weight: 735.46 kDa
Atom Count: 40,726
Modeled Residue Count: 5,399
Deposited Residue Count: 5,399
Unique protein chains: 14
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPB	A	720	Homo sapiens	Mutation(s): 0 Gene Names: ERCC3 EC: 5.6.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for P19447 (Homo sapiens) Explore P19447 Go to UniProtKB: P19447
PHAROS: P19447 GTEx: ENSG00000163161
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19447
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription and DNA repair factor IIH helicase subunit XPD	B	760	Homo sapiens	Mutation(s): 0 Gene Names: ERCC2 EC: 5.6.2.3
UniProt & NIH Common Fund Data Resources
Find proteins for P18074 (Homo sapiens) Explore P18074 Go to UniProtKB: P18074
PHAROS: P18074 GTEx: ENSG00000104884
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18074
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 4	C	441	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92759 (Homo sapiens) Explore Q92759 Go to UniProtKB: Q92759
PHAROS: Q92759 GTEx: ENSG00000213780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92759
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 2	D	377	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H2
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Find proteins for Q13888 (Homo sapiens) Explore Q13888 Go to UniProtKB: Q13888
GTEx: ENSG00000145736
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13888
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 3	E	292	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13889 (Homo sapiens) Explore Q13889 Go to UniProtKB: Q13889
PHAROS: Q13889 GTEx: ENSG00000111358
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13889
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 5	F	66	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZYL4 (Homo sapiens) Explore Q6ZYL4 Go to UniProtKB: Q6ZYL4
PHAROS: Q6ZYL4 GTEx: ENSG00000272047
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6ZYL4
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein complementing XP-A cells	G	273	Homo sapiens	Mutation(s): 0 Gene Names: XPA
UniProt & NIH Common Fund Data Resources
Find proteins for P23025 (Homo sapiens) Explore P23025 Go to UniProtKB: P23025
PHAROS: P23025 GTEx: ENSG00000136936
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23025
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 1	H	154	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H1
UniProt & NIH Common Fund Data Resources
Find proteins for P32780 (Homo sapiens) Explore P32780 Go to UniProtKB: P32780
PHAROS: P32780 GTEx: ENSG00000110768
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32780
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-5	I	985	Homo sapiens	Mutation(s): 0 Gene Names: ERCC5 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28715 (Homo sapiens) Explore P28715 Go to UniProtKB: P28715
PHAROS: P28715 GTEx: ENSG00000134899
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28715
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair endonuclease XPF Gene: ERCC4, ERCC11, XPF	J	227	Homo sapiens	Mutation(s): 0 Gene Names: ERCC4 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92889 (Homo sapiens) Explore Q92889 Go to UniProtKB: Q92889
PHAROS: Q92889 GTEx: ENSG00000175595
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92889
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair	K	198	Homo sapiens	Mutation(s): 0 Gene Names: ERCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P07992 (Homo sapiens) Explore P07992 Go to UniProtKB: P07992
PHAROS: P07992 GTEx: ENSG00000012061
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07992
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit, N-terminally processed	L	434	Homo sapiens	Mutation(s): 0 Gene Names: RPA1
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens) Explore P27694 Go to UniProtKB: P27694
PHAROS: P27694 GTEx: ENSG00000132383
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27694
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 14 kDa subunit	M	115	Homo sapiens	Mutation(s): 0 Gene Names: RPA3
UniProt & NIH Common Fund Data Resources
Find proteins for P35244 (Homo sapiens) Explore P35244 Go to UniProtKB: P35244
PHAROS: P35244 GTEx: ENSG00000106399
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35244
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 32 kDa subunit	N	225	Homo sapiens	Mutation(s): 0 Gene Names: RPA2
UniProt & NIH Common Fund Data Resources
Find proteins for P15927 (Homo sapiens) Explore P15927 Go to UniProtKB: P15927
PHAROS: P15927 GTEx: ENSG00000117748
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15927
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (66-MER)	O [auth X]	66	N/A
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
DNA (66-MER)	P [auth Y]	66	N/A
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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 Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain Q [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth L] SDF format, chain W [auth G] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] MOL2 format, chain Z [auth L] MOL2 format, chain W [auth G] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] mmCIF format, chain Z [auth L] mmCIF format, chain W [auth G] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D]	R [auth D] S [auth D] T [auth D] U [auth E] V [auth E] R [auth D], S [auth D], T [auth D], U [auth E], V [auth E], W [auth G], Z [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth G] Focus chain Z [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth J] SDF format, chain X [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth I]	X [auth I], Y [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain X [auth I] Focus chain Y [auth J]