7Z6H | pdb_00007z6h

Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 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

Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction.

Day, M.Oliver, A.W.Pearl, L.H.

(2022) Nucleic Acids Res 50: 8279-8289

  • DOI: https://doi.org/10.1093/nar/gkac588
  • Primary Citation of Related Structures:  
    7Z6H

  • PubMed Abstract: 

    The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5'-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5' DNA end and fixes the orientation of 9-1-1 on the ssDNA.


  • Organizational Affiliation
    • Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell cycle checkpoint control protein RAD9A405Homo sapiensMutation(s): 0 
Gene Names: RAD9A
EC: 3.1.11.2
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PHAROS:  Q99638
GTEx:  ENSG00000172613 
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UniProt GroupQ99638
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17B,
H [auth K]
1,021Homo sapiensMutation(s): 0 
Gene Names: RAD1REC1RAD17R24L
EC: 3.1.11.2
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GTEx:  ENSG00000113456 
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GTEx:  ENSG00000152942 
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UniProt GroupsO60671O75943
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Checkpoint protein HUS1280Homo sapiensMutation(s): 0 
Gene Names: HUS1
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PHAROS:  O60921
GTEx:  ENSG00000136273 
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UniProt GroupO60921
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4363Homo sapiensMutation(s): 0 
Gene Names: RFC4
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GTEx:  ENSG00000163918 
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UniProt GroupP35249
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3356Homo sapiensMutation(s): 0 
Gene Names: RFC3
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GTEx:  ENSG00000133119 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2354Homo sapiensMutation(s): 0 
Gene Names: RFC2
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GTEx:  ENSG00000049541 
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UniProt GroupP35250
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5360Homo sapiensMutation(s): 0 
Gene Names: RFC5
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GTEx:  ENSG00000111445 
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Entity ID: 8
MoleculeChains LengthOrganismImage
Hairpin DNAI [auth X],
J [auth Y]
77synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC302/A14532
Cancer Research UKUnited KingdomC302/A24386

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary