7ST9

Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanisms of loading and release of the 9-1-1 checkpoint clamp.

Castaneda, J.C.Schrecker, M.Remus, D.Hite, R.K.

(2022) Nat Struct Mol Biol 29: 369-375

  • DOI: https://doi.org/10.1038/s41594-022-00741-7
  • Primary Citation of Related Structures:  
    7ST9, 7STB, 7STE

  • PubMed Abstract: 

    Single-stranded or double-stranded DNA junctions with recessed 5' ends serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATR Mec1 . However, the basis for 9-1-1's recruitment to 5' junctions is unclear. Here, we present structures of the yeast checkpoint clamp loader, Rad24-replication factor C (RFC), in complex with 9-1-1 and a 5' junction and in a post-ATP-hydrolysis state. Unexpectedly, 9-1-1 adopts both closed and planar open states in the presence of Rad24-RFC and DNA. Moreover, Rad24-RFC associates with the DNA junction in the opposite orientation of processivity clamp loaders with Rad24 exclusively coordinating the double-stranded region. ATP hydrolysis stimulates conformational changes in Rad24-RFC, leading to disengagement of DNA-loaded 9-1-1. Together, these structures explain 9-1-1's recruitment to 5' junctions and reveal new principles of sliding clamp loading.


  • Organizational Affiliation

    Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Checkpoint protein RAD24696Saccharomyces cerevisiae S288CMutation(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 cerevisiae S288CMutation(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 3340Saccharomyces cerevisiae S288CMutation(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 cerevisiae S288CMutation(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 cerevisiae S288CMutation(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 RAD17401Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAD17YOR368W
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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint protein 1646Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DDC1YPL194W
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 proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage checkpoint control protein MEC3474Saccharomyces cerevisiae S288CMutation(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 nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (50-MER)I [auth J]50Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*CP*TP*CP*CP*TP*TP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*CP*C)-3')J [auth I]21Saccharomyces cerevisiae
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
K [auth A],
N [auth B],
R [auth C],
T [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 
U [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
O [auth C]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
THR
Query on THR

Download Ideal Coordinates CCD File 
P [auth C]THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

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)GM107239
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127428
National Institutes of Health/National Cancer Institute (NIH/NCI)CA008748

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
  • Version 1.3: 2024-06-05
    Changes: Data collection, Refinement description