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 
  • R-Value Observed: 0.239 

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Literature

Mechanism of DNA translocation in a replicative hexameric helicase.

Enemark, E.J., Joshua-Tor, L.

(2006) Nature 442: 270-275

  • DOI: https://doi.org/10.1038/nature04943
  • Primary Citation of Related Structures:  
    2GXA

  • 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 DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein E1274Deltapapillomavirus 4Mutation(s): 0 
Gene Names: E1
EC: 3.6.4.12
UniProt
Find proteins for P03116 (Bovine papillomavirus type 1)
Explore P03116 
Go to UniProtKB:  P03116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03116
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'A [auth M],
B [auth N]		13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
FA [auth H]
IA [auth J]
KA [auth K]
AA [auth F],
CA [auth G],
FA [auth H],
IA [auth J],
KA [auth K],
LA [auth L],
Q [auth A],
T [auth B],
V [auth C],
X [auth D],
Z [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
EA [auth H],
P [auth A],
S [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
GA [auth I]
HA [auth J]
JA [auth K]
BA [auth G],
DA [auth H],
GA [auth I],
HA [auth J],
JA [auth K],
O [auth A],
R [auth B],
U [auth C],
W [auth D],
Y [auth E]
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 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.51α = 92.6
b = 100.881β = 111.46
c = 125.023γ = 106.01
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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