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

--

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

View Full Validation Report or Ramachandran Plots



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