1JEK

Visna TM CORE STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The trimer-of-hairpins motif in membrane fusion: Visna virus.

Malashkevich, V.N.Singh, M.Kim, P.S.

(2001) Proc.Natl.Acad.Sci.USA 98: 8502-8506

  • DOI: 10.1073/pnas.151254798

  • PubMed Abstract: 
  • Structural studies of viral membrane fusion proteins suggest that a "trimer-of-hairpins" motif plays a critical role in the membrane fusion process of many enveloped viruses. In this motif, a coiled coil (formed by homotrimeric association of the N-t ...

    Structural studies of viral membrane fusion proteins suggest that a "trimer-of-hairpins" motif plays a critical role in the membrane fusion process of many enveloped viruses. In this motif, a coiled coil (formed by homotrimeric association of the N-terminal regions of the protein) is surrounded by three C-terminal regions that pack against the coiled coil in an oblique antiparallel manner. The resulting trimer-of-hairpins structure serves to bring the viral and cellular membranes together for fusion. learncoil-vmf, a computational program developed to recognize coiled coil-like regions that form the trimer-of-hairpins motif, predicts these regions in the membrane fusion protein of the Visna virus. Peptides corresponding to the computationally identified sequences were synthesized, and the soluble core of the Visna membrane fusion protein was reconstituted in solution. Its crystal structure at 1.5-A resolution demonstrates that a trimer-of-hairpins structure is formed. Remarkably, despite less than 23% sequence identity, the ectodomains in Visna and HIV-1 envelope glycoproteins show detailed structural conservation, especially within the area of a hydrophobic pocket in the central coiled coil currently being targeted for the development of new anti-HIV drugs.


    Related Citations: 
    • Crystal Structure of the Simian Immunodeficiency Virus (Siv) Gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of Gp41 Peptides
      Malashkevich, V.N.,Chan, D.C.,Chutkowski, C.T.,Kim, P.S.
      (1998) Proc.Natl.Acad.Sci.USA 95: 9134
    • Core Structure of Gp41 from the HIV Envelope Glycoprotein
      Chan, D.C.,Fass, D.,Berger, J.M.,Kim, P.S.
      (1997) Cell 89: 263


    Organizational Affiliation

    Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142-1401, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENV POLYPROTEIN
A
42Maedi visna virus (strain KV1772)Gene Names: env
Find proteins for P35954 (Maedi visna virus (strain KV1772))
Go to UniProtKB:  P35954
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENV POLYPROTEIN
B
36Maedi visna virus (strain KV1772)Gene Names: env
Find proteins for P35954 (Maedi visna virus (strain KV1772))
Go to UniProtKB:  P35954
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.548α = 90.00
b = 52.548β = 90.00
c = 61.686γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model