5VVR

Ternary complex of RNA Pol II, transcription scaffold and Rad26


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.

Xu, J.Lahiri, I.Wang, W.Wier, A.Cianfrocco, M.A.Chong, J.Hare, A.A.Dervan, P.B.DiMaio, F.Leschziner, A.E.Wang, D.

(2017) Nature 551: 653-657

  • DOI: 10.1038/nature24658
  • Primary Citation of Related Structures:  
    5VVR, 5VVS

  • PubMed Abstract: 
  • Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR ...

    Eukaryotic transcription-coupled repair (TCR) is an important and well-conserved sub-pathway of nucleotide excision repair that preferentially removes DNA lesions from the template strand that block translocation of RNA polymerase II (Pol II). Cockayne syndrome group B (CSB, also known as ERCC6) protein in humans (or its yeast orthologues, Rad26 in Saccharomyces cerevisiae and Rhp26 in Schizosaccharomyces pombe) is among the first proteins to be recruited to the lesion-arrested Pol II during the initiation of eukaryotic TCR. Mutations in CSB are associated with the autosomal-recessive neurological disorder Cockayne syndrome, which is characterized by progeriod features, growth failure and photosensitivity. The molecular mechanism of eukaryotic TCR initiation remains unclear, with several long-standing unanswered questions. How cells distinguish DNA lesion-arrested Pol II from other forms of arrested Pol II, the role of CSB in TCR initiation, and how CSB interacts with the arrested Pol II complex are all unknown. The lack of structures of CSB or the Pol II-CSB complex has hindered our ability to address these questions. Here we report the structure of the S. cerevisiae Pol II-Rad26 complex solved by cryo-electron microscopy. The structure reveals that Rad26 binds to the DNA upstream of Pol II, where it markedly alters its path. Our structural and functional data suggest that the conserved Swi2/Snf2-family core ATPase domain promotes the forward movement of Pol II, and elucidate key roles for Rad26 in both TCR and transcription elongation.


    Organizational Affiliation

    Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04050 
Go to UniProtKB:  P04050
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08518 
Go to UniProtKB:  P08518
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3YIL021W
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16370 
Go to UniProtKB:  P16370
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB4YJL140WJ0654
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20433 
Go to UniProtKB:  P20433
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB7YDR404CD9509.22
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34087 
Go to UniProtKB:  P34087
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9YGL070C
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27999 
Go to UniProtKB:  P27999
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11YOL005C
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38902 
Go to UniProtKB:  P38902
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair and recombination protein RAD26M1085Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD26GTA1085YJR035WJ1606
EC: 3.6.4.12
UniProt
Find proteins for P40352 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40352 
Go to UniProtKB:  P40352
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (NTS)N47Saccharomyces cerevisiae
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 15
    MoleculeChainsLengthOrganismImage
    RNAO [auth R]10Saccharomyces cerevisiae
    Protein Feature View
    Expand
    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 16
    MoleculeChainsLengthOrganismImage
    DNA (TS)P [auth T]47Saccharomyces cerevisiae
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 5.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102362

    Revision History  (Full details and data files)

    • Version 1.0: 2017-11-22
      Type: Initial release
    • Version 1.1: 2017-12-06
      Changes: Database references
    • Version 1.2: 2017-12-13
      Changes: Database references
    • Version 1.3: 2020-01-01
      Changes: Author supporting evidence