2GXA

Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of DNA translocation in a replicative hexameric helicase.

Enemark, E.J.Joshua-Tor, L.

(2006) Nature 442: 270-275

  • DOI: 10.1038/nature04943

  • PubMed Abstract: 
  • The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded ...

    The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.


    Organizational Affiliation

    W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Replication protein E1
A, B, C, D, E, F, G, H, I, J, K, L
274Bovine papillomavirus type 1Mutation(s): 0 
Gene Names: E1
EC: 3.6.4.12
Find proteins for P03116 (Bovine papillomavirus type 1)
Go to UniProtKB:  P03116
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'M,N13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, J, K, L
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.239 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 100.510α = 92.60
b = 100.881β = 111.46
c = 125.023γ = 106.01
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance