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 

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This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HERV-FRD_6p24.1 provirus ancestral Env polyproteinA, B, C53Homo sapiensMutation(s): 0 
Gene Names: ERVFRDE1ERVFRD-1UNQ6191/PRO20218
UniProt & NIH Common Fund Data Resources
Find proteins for P60508 (Homo sapiens)
Explore P60508 
Go to UniProtKB:  P60508
PHAROS:  P60508
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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

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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