1YPY | pdb_00001ypy

Crystal Structure of Vaccinia Virus L1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.246 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The 1.51-Angstrom structure of the poxvirus L1 protein, a target of potent neutralizing antibodies.

Su, H.P.Garman, S.C.Allison, T.J.Fogg, C.Moss, B.Garboczi, D.N.

(2005) Proc Natl Acad Sci U S A 102: 4240-4245

  • DOI: https://doi.org/10.1073/pnas.0501103102
  • Primary Citation of Related Structures:  
    1YPY

  • PubMed Abstract: 

    Although eradicated from nature more than two decades ago, the threat of smallpox has reemerged because of concerns over its use as a biological weapon. We present the structure of the poxvirus L1 protein, a molecule that is conserved throughout the poxvirus family and is nearly identical in vaccinia virus and in variola virus, which causes smallpox. L1 is a myristoylated envelope protein that is a potent target for neutralizing antibodies and an important component of current experimental vaccines. The L1 structure reveals a hydrophobic cavity located adjacent to its N terminus. The cavity would be capable of shielding the myristate moiety, which is essential for virion assembly. The structure of L1 is a step in the elucidation of molecular mechanisms common to all poxviruses that may stimulate the design of safer vaccines and new antipoxvirus drugs.


  • Organizational Affiliation
    • Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virion membrane protein
A, B
184Orthopoxvirus vacciniaMutation(s): 0 
Gene Names: L1
UniProt
Find proteins for P07612 (Vaccinia virus (strain Western Reserve))
Explore P07612 
Go to UniProtKB:  P07612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07612
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.246 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.746α = 90
b = 56.627β = 129.31
c = 72.557γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Structure summary