6RX3 | pdb_00006rx3

Crystal structure of human syncytin 2 in post-fusion conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.256 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RX3

This is version 1.3 of the entry. See complete history

Literature

X-ray Structures of the Post-fusion 6-Helix Bundle of the Human Syncytins and their Functional Implications.

Ruigrok, K.Vaney, M.C.Buchrieser, J.Baquero, E.Hellert, J.Baron, B.England, P.Schwartz, O.Rey, F.A.Backovic, M.

(2019) J Mol Biology 431: 4922-4940

  • DOI: https://doi.org/10.1016/j.jmb.2019.10.020
  • Primary Citation Related Structures: 
    6RX1, 6RX3

  • PubMed Abstract: 

    The retroviral envelope-derived proteins syncytin-1 and syncytin-2 (syn1 and syn2) drive placentation in humans by forming a syncytiotophoblast, a structure allowing for an exchange interface between maternal and fetal blood during pregnancy. Despite their essential role, little is known about the molecular mechanism underlying the syncytins' function. We report here the X-ray structures of the syn1 and syn2 transmembrane subunit ectodomains, featuring a 6-helix bundle (6HB) typical of the post-fusion state of gamma-retrovirus and filovirus fusion proteins. Contrary to the filoviruses, for which the fusion glycoprotein was crystallized both in the post-fusion and in the spring-loaded pre-fusion form, the highly unstable nature of the syncytins' prefusion form has precluded structural studies. We undertook a proline-scanning approach searching for regions in the syn1 6HB central helix that tolerate the introduction of helix-breaker residues and still fold correctly in the pre-fusion form. We found that there is indeed such a region, located two α-helical turns downstream a stutter in the central coiled-coil helix - precisely where the breaks of the spring-loaded helix of the filoviruses map. These mutants were fusion-inactive as they cannot form the 6HB, similar to the "SOSIP" mutant of HIV Env that allowed the high-resolution structural characterization of its labile pre-fusion form. These results now open a new window of opportunity to engineer more stable variants of the elusive pre-fusion trimer of the syncytins and other gamma-retroviruses envelope proteins for structural characterization.


  • Organizational Affiliation
    • Unité de Virologie Structurale, Institut Pasteur, Département de Virologie, 28 rue du Dr Roux, 75015 Paris, France; CNRS, UMR3569, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 36.63 kDa 
  • Atom Count: 2,233 
  • Modeled Residue Count: 274 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Syncytin-2
A, B, C
108Homo sapiensMutation(s): 0 
Gene Names: ERVFRD-1ERVFRDE1UNQ6191/PRO20218
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
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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: 2.20 Å
  • R-Value Free:  0.256 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.416α = 90
b = 91.416β = 90
c = 69.725γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance340371

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary