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 8TUG | pdb_00008tug

Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TUG

This is version 1.1 of the entry. See complete history. 

Literature

Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.

Sarsam, R.D., Xu, J., Lahiri, I., Gong, W., Li, Q., Oh, J., Zhou, Z., Hou, P., Chong, J., Hao, N., Li, S., Wang, D., Leschziner, A.E.

(2024) Proc Natl Acad Sci U S A 121: e2314245121-e2314245121

  • DOI: https://doi.org/10.1073/pnas.2314245121
  • Primary Citation Related Structures: 
    8TUG, 8TVP, 8TVQ, 8TVS, 8TVV, 8TVW, 8TVX, 8TVY

  • PubMed Abstract: 

    Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.


  • Organizational Affiliation: 
    • Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093.

Macromolecule Content 

  • Total Structure Weight: 589.57 kDa 
  • Atom Count: 34,436 
  • Modeled Residue Count: 4,354 
  • Deposited Residue Count: 5,171 
  • Unique protein chains: 13
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP04050
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP08518
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP16370
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20433
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20434
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20435
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP34087
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20436
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP27999
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II subunit RPABC570Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38902
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases II subunit RPABC470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40422
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair and recombination protein RAD26503Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (NTS)47synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (TS)O [auth T]46synthetic construct
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Reference Sequence
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Entity ID: 16
MoleculeChains LengthOrganismImage
RNAP [auth R]10synthetic construct
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
Q [auth A]
R [auth A]
T [auth B]
U [auth C]
V [auth I]
Q [auth A],
R [auth A],
T [auth B],
U [auth C],
V [auth I],
W [auth I],
X [auth J],
Y [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
S [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
M
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 StatesR01 GM092895
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM145296
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM102362
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM092895

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection, Structure summary