7OPD

Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural basis of human transcription-DNA repair coupling.

Kokic, G.Wagner, F.R.Chernev, A.Urlaub, H.Cramer, P.

(2021) Nature 598: 368-372

  • DOI: https://doi.org/10.1038/s41586-021-03906-4
  • Primary Citation of Related Structures:  
    7OO3, 7OOB, 7OOP, 7OPC, 7OPD

  • PubMed Abstract: 

    Transcription-coupled DNA repair removes bulky DNA lesions from the genome 1,2 and protects cells against ultraviolet (UV) irradiation 3 . Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 CSA and UV-stimulated scaffold protein A (UVSSA) 3 . Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published 3,4 data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC TCR , uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Sus scrofaMutation(s): 0 
EC: 3.1.13 (UniProt), 2.7.7.48 (UniProt), 2.7.7.6 (UniProt)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RPOL4c domain-containing protein142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit F127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing protein117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT61,729Homo sapiensMutation(s): 0 
Gene Names: SUPT6HKIAA0162SPT6H
UniProt & NIH Common Fund Data Resources
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GTEx:  ENSG00000109111 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
LEO1 helixP [auth R]40Homo sapiensMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homologQ [auth S]1,179Homo sapiensMutation(s): 0 
Gene Names: CTR9KIAA0155SH2BP1
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GTEx:  ENSG00000198730 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein LEO1S [auth U]666Homo sapiensMutation(s): 0 
Gene Names: LEO1RDL
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GTEx:  ENSG00000166477 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated factor 1 homologT [auth V]531Homo sapiensMutation(s): 0 
Gene Names: PAF1PD2
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GTEx:  ENSG00000006712 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 61U [auth Y]305Homo sapiensMutation(s): 0 
Gene Names: WDR61
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GTEx:  ENSG00000140395 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ParafibrominV [auth Z]531Homo sapiensMutation(s): 0 
Gene Names: CDC73C1orf28HRPT2
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GTEx:  ENSG00000134371 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8W [auth a]396Homo sapiensMutation(s): 0 
Gene Names: ERCC8CKN1CSA
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PHAROS:  Q13216
GTEx:  ENSG00000049167 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-6X [auth b]1,496Homo sapiensMutation(s): 0 
Gene Names: ERCC6CSB
EC: 3.6.4
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PHAROS:  Q03468
GTEx:  ENSG00000225830 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
UV-stimulated scaffold protein AY [auth c]712Homo sapiensMutation(s): 0 
Gene Names: UVSSAKIAA1530
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PHAROS:  Q2YD98
GTEx:  ENSG00000163945 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1Z [auth d]1,143Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
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PHAROS:  Q16531
GTEx:  ENSG00000167986 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-4AAA [auth e]762Homo sapiensMutation(s): 0 
Gene Names: CUL4A
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GTEx:  ENSG00000139842 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1BA [auth f]108Mus musculusMutation(s): 0 
Gene Names: Rbx1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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Entity ID: 14
MoleculeChains LengthOrganismImage
NTS47Homo sapiens
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNAO [auth P]45Homo sapiens
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Entity ID: 18
MoleculeChains LengthOrganismImage
TSR [auth T]47Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
FA [auth B]
GA [auth C]
HA [auth I]
CA [auth A],
DA [auth A],
FA [auth B],
GA [auth C],
HA [auth I],
IA [auth I],
JA [auth J],
KA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2067/1 39072994, SFB860, SPP2191
European Research Council (ERC)Germany882357

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 2.0: 2021-10-13
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Data collection, Database references
  • Version 2.2: 2024-07-17
    Changes: Data collection