8FS4 | pdb_00008fs4

Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 2 (open 9-1-1 ring and flexibly bound chamber DNA)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history. 


Literature

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

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

(2023) Cell Rep 42: 112694-112694

  • DOI: https://doi.org/10.1016/j.celrep.2023.112694
  • Primary Citation Related Structures: 
    8FS3, 8FS4, 8FS5, 8FS6, 8FS7, 8FS8

  • PubMed Abstract: 

    Rad24-RFC (replication factor C) loads the 9-1-1 checkpoint clamp onto the recessed 5' ends by binding a 5' DNA at an external surface site and threading the 3' single-stranded DNA (ssDNA) into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' end, thus presumably leaving 9-1-1 on duplex 3' ss/double-stranded DNA (dsDNA) after Rad24-RFC ejects from DNA. We captured five Rad24-RFC-9-1-1 loading intermediates using a 10-nt gap DNA. We also determined the structure of Rad24-RFC-9-1-1 using a 5-nt gap DNA. The structures reveal that Rad24-RFC is unable to melt DNA ends and that a Rad24 loop limits the dsDNA length in the chamber. These observations explain Rad24-RFC's preference for a preexisting gap of over 5-nt ssDNA and suggest a direct role of the 9-1-1 in gap repair with various TLS (trans-lesion synthesis) polymerases in addition to signaling the ATR kinase.

    • Organizational Affiliation: 
    • Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Checkpoint protein RAD24544Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD24, YER173W, SYGP-ORF60
UniProt
Find proteins for P32641 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32641
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4323Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC4, YOL094C, O0923
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3336Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3, YNL290W, N0533
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2, YJR068W, J1808
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40348
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC5, YBR087W, YBR0810
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein MEC3474Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MEC3, PIP3, PSO9, YLR288C, L8003.15
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein RAD17401Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD17, GI527_G0005737
UniProt
Find proteins for P48581 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DDC1 isoform 1612Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DDC1
UniProt
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Entity ID: 9
MoleculeChains LengthOrganismImage
Template strand50synthetic construct
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Entity ID: 10
MoleculeChains LengthOrganismImage
Primer strand 121synthetic construct
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Entity ID: 11
MoleculeChains LengthOrganismImage
Primer strand 220synthetic construct
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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
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T [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG
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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: 2.94 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
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
  • Version 1.2: 2025-06-04
    Changes: Data collection, Structure summary
  • Version 1.3: 2026-04-29
    Changes: Data collection, Database references