6GIS

Structural basis of human clamp sliding on DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5L7C - determined by De March, M., Merino, N., Barrera-Vilarmau, S., Crehuet, R., Onesti, S., Blanco, F.J., De Biasio, A.  

Literature

Structural basis of human PCNA sliding on DNA.

De March, M.Merino, N.Barrera-Vilarmau, S.Crehuet, R.Onesti, S.Blanco, F.J.De Biasio, A.

(2017) Nat Commun 8: 13935-13935

  • DOI: 10.1038/ncomms13935
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the hu ...

    Sliding clamps encircle DNA and tether polymerases and other factors to the genomic template. However, the molecular mechanism of clamp sliding on DNA is unknown. Using crystallography, NMR and molecular dynamics simulations, here we show that the human clamp PCNA recognizes DNA through a double patch of basic residues within the ring channel, arranged in a right-hand spiral that matches the pitch of B-DNA. We propose that PCNA slides by tracking the DNA backbone via a 'cogwheel' mechanism based on short-lived polar interactions, which keep the orientation of the clamp invariant relative to DNA. Mutation of residues at the PCNA-DNA interface has been shown to impair the initiation of DNA synthesis by polymerase δ (pol δ). Therefore, our findings suggest that a clamp correctly oriented on DNA is necessary for the assembly of a replication-competent PCNA-pol δ holoenzyme.


    Related Citations: 
    • Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.
      De Biasio, A.,de Opakua, A.I.,Mortuza, G.B.,Molina, R.,Cordeiro, T.N.,Castillo, F.,Villate, M.,Merino, N.,Delgado, S.,Gil-Carton, D.,Luque, I.,Diercks, T.,Bernado, P.,Montoya, G.,Blanco, F.J.
      (2015) Nat Commun 6: 6439


    Organizational Affiliation

    Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., 34149 Trieste, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C
261Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
B
262Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')D10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')E10synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 180.189α = 90.00
b = 180.189β = 90.00
c = 76.832γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release