1Y4M

Crystal structure of human endogenous retrovirus HERV-FRD envelope protein (syncitin-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of a pivotal domain of human syncytin-2, a 40 million years old endogenous retrovirus fusogenic envelope gene captured by primates.

Renard, M.Varela, P.F.Letzelter, C.Duquerroy, S.Rey, F.A.Heidmann, T.

(2005) J Mol Biol 352: 1029-1034

  • DOI: https://doi.org/10.1016/j.jmb.2005.07.058
  • Primary Citation of Related Structures:  
    1Y4M

  • PubMed Abstract: 

    HERV-FRD is a human endogenous retrovirus that entered the human genome 40 million years ago. Its envelope gene, syncytin-2, was diverted by an ancestral host most probably because of its fusogenic property, for a role in placenta morphogenesis. It was maintained in a functional state in all primate branches as a bona fide cellular gene, submitted to a very low mutation rate as compared to infectious retrovirus genomes. The structure of the syncytin-2 protein thus provides a good insight into that of the oldest mammalian retroviral envelope. Here, we report the crystal structure of a central fragment of its "fossil" ectodomain, allowing a remarkable superposition with the structures of the corresponding domains of present-day infectious retroviruses, in spite of a more than 60% divergent sequence. These results suggest the existence of a unique structural solution selected by these proteins for their fusogenic function.


  • Organizational Affiliation

    Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, UMR 8122 CNRS, Institut Gustave Roussy, 94805 Villejuif, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HERV-FRD_6p24.1 provirus ancestral Env polyprotein
A, B, C
53Homo sapiensMutation(s): 0 
Gene Names: ERVFRDE1
UniProt & NIH Common Fund Data Resources
Find proteins for P60508 (Homo sapiens)
Explore P60508 
Go to UniProtKB:  P60508
PHAROS:  P60508
GTEx:  ENSG00000244476 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60508
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.404α = 90
b = 90.404β = 90
c = 38.654γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-15
    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: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary