2V9P

Crystal structure of papillomavirus E1 hexameric helicase DNA-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Papillomavirus E1 Helicase Assembly Maintains an Asymmetric State in the Absence of DNA and Nucleotide Cofactors.

Sanders, C.M.Kovalevskiy, O.V.Sizov, D.Lebedev, A.A.Isupov, M.N.Antson, A.A.

(2007) Nucleic Acids Res 35: 6451

  • DOI: 10.1093/nar/gkm705
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first ...

    Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.


    Organizational Affiliation

    Institute for Cancer Studies, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REPLICATION PROTEIN E1
A, B, C, D, E, F, G, H, I, J, K, L
305Deltapapillomavirus 4Mutation(s): 0 
Gene Names: E1
EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
Find proteins for P03116 (Bovine papillomavirus type 1)
Go to UniProtKB:  P03116
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, G, H, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.111α = 90
b = 180.649β = 90
c = 187.533γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance