2NTI

Crystal structure of PCNA123 heterotrimer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.

Hlinkova, V.Xing, G.Bauer, J.Shin, Y.J.Dionne, I.Rajashankar, K.R.Bell, S.D.Ling, H.

(2008) Acta Crystallogr.,Sect.D 64: 941-949

  • DOI: 10.1107/S0907444908021665
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA sliding clamps form an oligomeric ring encircling DNA and serve as a moving platform for DNA-processing proteins. The opening and closing of a sliding-clamp ring is essential to load the clamp onto DNA in order to perform its functions. The molec ...

    DNA sliding clamps form an oligomeric ring encircling DNA and serve as a moving platform for DNA-processing proteins. The opening and closing of a sliding-clamp ring is essential to load the clamp onto DNA in order to perform its functions. The molecular details of how clamp rings open and enclose DNA are still not clear. Three PCNA homologues have been found in Sulfolobus solfataricus which form a heterotrimer. Taking advantage of their hetero-oligomeric nature, the structures of the PCNAs in monomeric PCNA3, dimeric PCNA1-PCNA2 and trimeric PCNA1-PCNA2-PCNA3 forms were determined at resolutions of 2.6-1.9 A. The distinct oligomeric structures represent different stages in ring formation, which were verified in solution by ultracentrifugation analysis. The heterodimer opens in a V-shape of 130 degrees , while the heterotrimers form a ring with a 120 degrees rotation between monomers. The association of a rigid PCNA3 monomer with an opened PCNA1-PCNA2 heterodimer closes the ring and introduces a spring tension in the PCNA1-PCNA2 interface, thus bending the nine-stranded intermolecular beta-sheet to fit the 120 degrees rotation. The release of the spring tension as PCNA3 dissociates from the ring may facilitate ring opening. The structural features in different assemblies present a molecular model for clamp ring assembly and opening.


    Organizational Affiliation

    Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase sliding clamp B
D, A, G
249Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 1 
Gene Names: pcn1 (pcnA-like)
Find proteins for P57766 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P57766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase sliding clamp C
E, B, H
246Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: pcn2 (pcnA-2)
Find proteins for Q97Z84 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97Z84
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase sliding clamp A
F, C, I
244Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: pcn3 (pcnA-1)
Find proteins for P57765 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P57765
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
7PG
Query on 7PG

Download SDF File 
Download CCD File 
H
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL
C17 H36 O9
SZGNWRSFHADOMY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 148.140α = 90.00
b = 222.330β = 90.00
c = 80.230γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-07 
  • Released Date: 2007-12-18 
  • Deposition Author(s): Hlinkova, V., Ling, H.

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance