1QBZ

THE CRYSTAL STRUCTURE OF THE SIV GP41 ECTODOMAIN AT 1.47 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.218 
  • R-Value Observed: 0.152 

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This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the SIV gp41 ectodomain at 1.47 A resolution.

Yang, Z.N.Mueser, T.C.Kaufman, J.Stahl, S.J.Wingfield, P.T.Hyde, C.C.

(1999) J Struct Biol 126: 131-144

  • DOI: 10.1006/jsbi.1999.4116
  • Primary Citation of Related Structures:  
    1QBZ

  • PubMed Abstract: 
  • Cell membrane fusion by human (HIV) and simian (SIV) immunodeficiency viruses is mediated by the envelope glycoproteins gp120 and gp41. Although the precise mechanism of the fusion process is unknown, the ectodomain of gp41 is thought to undergo dramatic rearrangement from its prefusogenic state ...

    Cell membrane fusion by human (HIV) and simian (SIV) immunodeficiency viruses is mediated by the envelope glycoproteins gp120 and gp41. Although the precise mechanism of the fusion process is unknown, the ectodomain of gp41 is thought to undergo dramatic rearrangement from its prefusogenic state. To elucidate this process further, the crystal structure of the SIV gp41 ectodomain (residues 27-149) was determined at 1.47 A resolution and is reported herein. It is the most accurate and complete structure of a retroviral gp41 ectodomain determined to date. The rod-like trimeric structure of SIV gp41 comprises three parallel N-terminal alpha-helices assembled as a coiled coil in the center with three antiparallel C-terminal alpha-helices packed on the outside connected by highly flexible loops. Portions of the loops in all three monomers are crystallographically disordered and could not be accurately modeled. The core of the structure is similar (but not identical) to those of smaller HIV/SIV gp41 segments previously determined by X-ray crystallography with root mean square deviations in main chain atoms of less than 1.0 A. The crystal structure differs more substantially from the reported NMR solution structure of the identical SIV construct. The mechanisms of viral fusion and the inhibition by peptides are discussed in the context of the three-dimensional structure.


    Organizational Affiliation

    Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland 20892, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SIV GP41 ECTODOMAIN)A, B, C123Simian immunodeficiency virusMutation(s): 2 
Gene Names: env
UniProt
Find proteins for E7CWP5 (Simian immunodeficiency virus)
Explore E7CWP5 
Go to UniProtKB:  E7CWP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7CWP5
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.218 
  • R-Value Observed: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.124α = 90
b = 47.206β = 100.83
c = 77.465γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
DMphasing
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-12-16
    Changes: Atomic model