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 

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
  • 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein E1274Deltapapillomavirus 4Mutation(s): 0 
Gene Names: E1
EC: 3.6.4.12
Find proteins for P03116 (Bovine papillomavirus type 1)
Explore P03116 
Go to UniProtKB:  P03116
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • 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
    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] , LA [auth L] , Q [auth A] , T [auth B] , 
    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] , O [auth A] , R [auth B] , U [auth C] , 
    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

    View Full Validation Report



    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