1SXJ

Crystal Structure of the Eukaryotic Clamp Loader (Replication Factor C, RFC) Bound to the DNA Sliding Clamp (Proliferating Cell Nuclear Antigen, PCNA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex.

Bowman, G.D., O'Donnell, M., Kuriyan, J.

(2004) Nature 429: 724-730

  • DOI: 10.1038/nature02585

  • PubMed Abstract: 

    • Sliding clamps are ring-shaped proteins that encircle DNA and confer high processivity on DNA polymerases. Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae ...

    Sliding clamps are ring-shaped proteins that encircle DNA and confer high processivity on DNA polymerases. Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, PCNA). Tight interfacial coordination of the ATP analogue ATP-gammaS by RFC results in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA reveals a striking correspondence between the RFC spiral and the grooves of the DNA double helix. This model, in which the clamp loader complex locks onto primed DNA in a screw-cap-like arrangement, provides a simple explanation for the process by which the engagement of primer-template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Activator 1 95 kDa subunit
A
516Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RFC1 (CDC44)
Find proteins for P38630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RFC1
Go to UniProtKB:  P38630
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Activator 1 37 kDa subunit
B
323Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: RFC4
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RFC4
Go to UniProtKB:  P40339
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Activator 1 40 kDa subunit
C
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: RFC3
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RFC3
Go to UniProtKB:  P38629
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Activator 1 41 kDa subunit
D
353Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: RFC2
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RFC2
Go to UniProtKB:  P40348
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Activator 1 40 kDa subunit
E
354Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: RFC5
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RFC5
Go to UniProtKB:  P38251
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
F, G, H
283Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: POL30
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P15873
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download SDF File 
Download CCD File 
E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS
Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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MSE
Query on MSE
F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 104.209α = 90.00
b = 110.481β = 90.00
c = 268.206γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
SOLVEphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance