8FS8

Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology.

Zheng, F.Georgescu, R.E.Yao, N.Y.O'Donnell, M.E.Li, H.

(2023) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.05.03.539266
  • Primary Citation of Related Structures:  
    8FS3, 8FS4, 8FS5, 8FS6, 8FS7, 8FS8

  • PubMed Abstract: 

    Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Checkpoint protein RAD24499Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD24YER173WSYGP-ORF60
UniProt
Find proteins for P32641 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32641 
Go to UniProtKB:  P32641
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32641
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4323Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC4YOL094CO0923
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40339 
Go to UniProtKB:  P40339
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40339
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3336Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3YNL290WN0533
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38629 
Go to UniProtKB:  P38629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38629
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2YJR068WJ1808
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40348 
Go to UniProtKB:  P40348
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40348
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC5YBR087WYBR0810
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38251 
Go to UniProtKB:  P38251
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38251
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein MEC3474Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MEC3PIP3PSO9YLR288CL8003.15
UniProt
Find proteins for Q02574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02574 
Go to UniProtKB:  Q02574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02574
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein RAD17401Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD17GI527_G0005737
UniProt
Find proteins for P48581 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48581 
Go to UniProtKB:  P48581
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48581
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DDC1 isoform 1612Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DDC1
UniProt
Find proteins for Q08949 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08949 
Go to UniProtKB:  Q08949
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08949
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains LengthOrganismImage
Template strand50synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 10
MoleculeChains LengthOrganismImage
Primer strand 120synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 11
MoleculeChains LengthOrganismImage
Primer strand 220synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
P [auth C],
R [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
T [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth A],
O [auth B],
Q [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 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 StatesGM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115809
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection