8EBT

XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.

Kim, J.Li, C.L.Chen, X.Cui, Y.Golebiowski, F.M.Wang, H.Hanaoka, F.Sugasawa, K.Yang, W.

(2023) Nature 617: 170-175

  • DOI: https://doi.org/10.1038/s41586-023-05959-z
  • Primary Citation of Related Structures:  
    8EBS, 8EBT, 8EBU, 8EBV, 8EBW, 8EBX, 8EBY

  • PubMed Abstract: 

    Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts 1 . After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases 2 . Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported 3-7 . How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.


  • Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPB603Homo sapiensMutation(s): 0 
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PHAROS:  P19447
GTEx:  ENSG00000163161 
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UniProt GroupP19447
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPD730Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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GTEx:  ENSG00000104884 
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UniProt GroupP18074
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1438Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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GTEx:  ENSG00000110768 
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UniProt GroupP32780
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4446Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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GTEx:  ENSG00000213780 
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UniProt GroupQ92759
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2380Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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GTEx:  ENSG00000145736 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3284Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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GTEx:  ENSG00000111358 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 566Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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GTEx:  ENSG00000272047 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein complementing XP-C cells274Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154767 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Centrin-2I [auth J]70Homo sapiensMutation(s): 0 
Gene Names: CETN2CALTCEN2
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GTEx:  ENSG00000147400 
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UniProt GroupP41208
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein complementing XP-A cellsJ [auth K]172Homo sapiensMutation(s): 0 
Gene Names: XPAXPAC
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GTEx:  ENSG00000136936 
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Entity ID: 11
MoleculeChains LengthOrganismImage
DNA (Cy5)K [auth L]44synthetic construct
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNAL [auth M]45synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
M [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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N [auth E]
O [auth E]
P [auth E]
Q [auth F]
R [auth F]
N [auth E],
O [auth E],
P [auth E],
Q [auth F],
R [auth F],
U [auth K]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
S [auth J],
T [auth J]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK075037
Japan Society for the Promotion of Science (JSPS)JapanJP16H06307
Japan Society for the Promotion of Science (JSPS)JapanJP21H03598

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references