9PD3 | pdb_00009pd3

NER dual incision complex - DuIS

PDB DOI: https://doi.org/10.2210/pdb9PD3/pdb
EM Map EMD-71524: EMDB EMDataResource
NAKB: 9PD3

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda, Escherichia coli BL21, Homo sapiens
Mutation(s): Yes

Deposited: 2025-06-30 Released: 2026-02-18
Deposition Author(s): Li, C.L., Kim, J., Yang, W.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Nucleotide Excision Repair Uncovered by Pre-incision Complex Structures

Li, C.L., Kim, J., Yang, W.

To be published.

Macromolecule Content

Total Structure Weight: 930.85 kDa
Atom Count: 35,072
Modeled Residue Count: 4,313
Deposited Residue Count: 8,055
Unique protein chains: 15
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TFIIH basal transcription factor complex helicase XPB subunit	A	782	Homo sapiens	Mutation(s): 0 Gene Names: ERCC3, XPB, XPBC EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19447
Sequence Annotations Expand
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	768	Homo sapiens	Mutation(s): 0 Gene Names: ERCC2, XPD, XPDC EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18074
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 1	C	548	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H1, BTF2
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32780
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 4, p52	D	462	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92759
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 2	E	395	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H2, BTF2P44
UniProt & NIH Common Fund Data Resources
Find proteins for Q13888 (Homo sapiens) Explore Q13888 Go to UniProtKB: Q13888
GTEx: ENSG00000145736
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13888
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 3	F	308	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13889
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIH subunit 5	G	71	Homo sapiens	Mutation(s): 0 Gene Names: GTF2H5, C6orf175, TTDA
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZYL4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein complementing XP-C cells	H	940	Homo sapiens	Mutation(s): 0 Gene Names: XPC, XPCC
UniProt & NIH Common Fund Data Resources
Find proteins for Q01831 (Homo sapiens) Explore Q01831 Go to UniProtKB: Q01831
PHAROS: Q01831 GTEx: ENSG00000154767
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01831
Sequence Annotations Expand
Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein complementing XP-A cells	I [auth K]	273	Homo sapiens	Mutation(s): 0 Gene Names: XPA, XPAC
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23025
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit	L [auth N]	616	Homo sapiens	Mutation(s): 0 Gene Names: RPA1, REPA1, RPA70
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27694
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 32 kDa subunit	M [auth O]	270	Homo sapiens	Mutation(s): 0 Gene Names: RPA2, REPA2, RPA32, RPA34
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15927
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 14 kDa subunit	N [auth P]	121	Homo sapiens	Mutation(s): 0 Gene Names: RPA3, REPA3, RPA14
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35244
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair endonuclease XPF	O [auth Q]	916	Homo sapiens	Mutation(s): 1 Gene Names: ERCC4, ERCC11, XPF 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92889
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-1	P [auth R]	295	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07992
Sequence Annotations Expand
Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-5	Q [auth S]	1,186	Homo sapiens	Mutation(s): 2 Gene Names: ERCC5, ERCM2, XPG, XPGC 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28715
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Length	Organism	Image
DNA lesion strand	J [auth L]	51	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Length	Organism	Image
DNA normal strand	K [auth M]	53	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth K] SDF format, chain Y [auth N] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth K] MOL2 format, chain Y [auth N] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth K] mmCIF format, chain Y [auth N]	S [auth E] T [auth E] U [auth E] V [auth F] W [auth F] S [auth E], T [auth E], U [auth E], V [auth F], W [auth F], X [auth K], Y [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth K] Focus chain Y [auth N] Interactions & Density Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth K] Focus chain Y [auth N]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.21rc1_5127

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Li, C.L.

Kim, J.

Yang, W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK075037

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9PD3 | pdb_00009pd3

NER dual incision complex - DuIS

Nucleotide Excision Repair Uncovered by Pre-incision Complex Structures

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

Sequence Annotations

Entity ID: 11

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9PD3 | pdb_00009pd3