Structure of the ASLV fusion subunit core

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Structural characterization of a fusion glycoprotein from a retrovirus that undergoes a hybrid 2-step entry mechanism.

Aydin, H.Smrke, B.M.Lee, J.E.

(2013) FASEB J 27: 5059-5071

  • DOI: https://doi.org/10.1096/fj.13-232371
  • Primary Citation of Related Structures:  
    4JPR, 5H9C

  • PubMed Abstract: 

    Entry of enveloped viruses into host cells is mediated by their surface envelope glycoproteins (Env). On the surface of the virus, Env is in a metastable, prefusion state, primed to catalyze the fusion of the viral and host membranes. An external trigger is needed to promote the drastic conformational changes necessary for the fusion subunit to fold into the low-energy, 6-helix bundle. These triggers typically facilitate pH-independent entry at the plasma membrane or pH-dependent entry in a low-pH endosomal compartment. The α-retrovirus avian sarcoma leukosis virus (ASLV) has a rare, 2-step entry mechanism with both pH-dependent and pH-independent features. Here, we present the 2.0-Å-resolution crystal structure of the ASLV transmembrane (TM) fusion protein. Our structural and biophysical studies indicated that unlike other pH-dependent or pH-independent viral TMs, the ASLV fusion subunit is stable irrespective of pH. Two histidine residues (His490 and His492) in the chain reversal region confer stability at low pH. A structural comparison of class I viral fusion proteins suggests that the presence of a positive charge, either a histidine or arginine amino acid, stabilizes a helical dipole moment and is a signature of fusion proteins active at low pH. The structure now reveals key residues and features that explain its 2-step mechanism, and we discuss the implications of the ASLV TM structure in the context of general mechanisms required for membrane fusion.

  • Organizational Affiliation

    11 King's College Cir., Rm. 6316, Toronto, ON, Canada M5S 1A8. jeff.lee@utoronto.ca.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASLV fusion TM95Rous sarcoma virus (strain Schmidt-Ruppin A)Mutation(s): 0 
Gene Names: env
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.544α = 90
b = 42.544β = 90
c = 119.982γ = 120
Software Package:
Software NamePurpose
d*TREKdata reduction
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2014-04-09
    Changes: Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description