7OOB

Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 

  • DOI: 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 ...

    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. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaB1174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RPOL4c domain-containing proteinD142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
UniProt
Find proteins for A0A287ADR4 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EE210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
UniProt
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FF127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
UniProt
Find proteins for F1SKN8 (Sus scrofa)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
UniProt
Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
UniProt
Find proteins for A0A4X1ULF2 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
UniProt
Find proteins for P60899 (Sus scrofa)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinK117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit KL58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-6M [auth b]1496Homo sapiensMutation(s): 0 
Gene Names: ERCC6CSB
EC: 3.6.4
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Find proteins for Q03468 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1N [auth d]1143Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA excision repair protein ERCC-8R [auth a]396Homo sapiensMutation(s): 0 
Gene Names: ERCC8CKN1CSA
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PHAROS:  Q13216
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  • Reference Sequence
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Entity ID: 15
MoleculeChainsLengthOrganismImage
NTSO [auth N]47Homo sapiens
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Entity ID: 16
MoleculeChainsLengthOrganismImage
TSP [auth T]47Homo sapiens
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  • Entity ID: 17
    MoleculeChainsLengthOrganismImage
    RNAQ [auth P]10Homo sapiens
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    • Reference Sequence
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP (Subject of Investigation/LOI)
    Query on ADP

    Download Ideal Coordinates CCD File 
    BA [auth b]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    BEF
    Query on BEF

    Download Ideal Coordinates CCD File 
    CA [auth b]BERYLLIUM TRIFLUORIDE ION
    Be F3
    OGIAHMCCNXDTIE-UHFFFAOYSA-K
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AA [auth L], S [auth A], T [auth A], V [auth B], W [auth C], X [auth I], Y [auth I], Z [auth J]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    DA [auth b], U [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.70 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2021-05-27 
    • Released Date: 2021-10-13 
    • Deposition Author(s): Kokic, G., Cramer, P.

    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: 2021-10-13
      Type: Initial release