7SGZ

Structure of the yeast Rad24-RFC loader bound to DNA and the closed 9-1-1 clamp


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp.

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

(2022) Nat Struct Mol Biol 29: 376-385

  • DOI: https://doi.org/10.1038/s41594-022-00742-6
  • Primary Citation of Related Structures:  
    7SGZ, 7SH2

  • PubMed Abstract: 

    The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring.


  • 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 RAD24659Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD24YER173WSYGP-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: RFC4YOL094CO0923
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 3340Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3YNL290WN0533
UniProt
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UniProt GroupP38629
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2YJR068WJ1808
UniProt
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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: RFC5YBR087WYBR0810
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitosis Entry Checkpoint protein MEC3460Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4067PACBIOSEQ_LOCUS4215SCNYR20_0004029900SCP684_0004029500
UniProt
Find proteins for Q02574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein RAD17401Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD17YOR368W
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA Damage Checkpoint protein DDC1593Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5976
UniProt
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Entity ID: 9
MoleculeChains LengthOrganismImage
Watson strandI [auth P]20synthetic construct
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Entity ID: 10
MoleculeChains LengthOrganismImage
Crick strandJ [auth T]40synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
O [auth C],
Q [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
S [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

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T [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

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L [auth A],
N [auth B],
P [auth C],
R [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2022-04-27
    Changes: Database references