4ADG

Crystal structure of the Rubella virus envelope Glycoprotein E1 in post-fusion form (crystal form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional and Evolutionary Insight from the Crystal Structure of Rubella Virus Protein E1.

Dubois, R.M.Vaney, M.C.Tortorici, M.A.Kurdi, R.A.Barba-Spaeth, G.Krey, T.Rey, F.A.

(2013) Nature 493: 552

  • DOI: 10.1038/nature11741
  • Primary Citation of Related Structures:  4ADI, 4ADJ, 4B3V

  • PubMed Abstract: 
  • Little is known about the three-dimensional organization of rubella virus, which causes a relatively mild measles-like disease in children but leads to serious congenital health problems when contracted in utero. Although rubella virus belongs to the ...

    Little is known about the three-dimensional organization of rubella virus, which causes a relatively mild measles-like disease in children but leads to serious congenital health problems when contracted in utero. Although rubella virus belongs to the same family as the mosquito-borne alphaviruses, in many respects it is more similar to other aerosol-transmitted human viruses such as the agents of measles and mumps. Although the use of the triple MMR (measles, mumps and rubella) live vaccine has limited its incidence in western countries, congenital rubella syndrome remains an important health problem in the developing world. Here we report the 1.8 Å resolution crystal structure of envelope glycoprotein E1, the main antigen and sole target of neutralizing antibodies against rubella virus. E1 is the main player during entry into target cells owing to its receptor-binding and membrane-fusion functions. The structure reveals the epitope and the neutralization mechanism of an important category of protecting antibodies against rubella infection. It also shows that rubella virus E1 is a class II fusion protein, which had hitherto only been structurally characterized for the arthropod-borne alphaviruses and flaviviruses. In addition, rubella virus E1 has an extensive membrane-fusion surface that includes a metal site, reminiscent of the T-cell immunoglobulin and mucin family of cellular proteins that bind phosphatidylserine lipids at the plasma membrane of cells undergoing apoptosis. Such features have not been seen in any fusion protein crystallized so far. Structural comparisons show that the class II fusion proteins from alphaviruses and flaviviruses, despite belonging to different virus families, are closer to each other than they are to rubella virus E1. This suggests that the constraints on arboviruses imposed by alternating cycles between vertebrates and arthropods resulted in more conservative evolution. By contrast, in the absence of this constraint, the strictly human rubella virus seems to have drifted considerably into a unique niche as sole member of the Rubivirus genus.


    Related Citations: 
    • Structure and Interactions at the Viral Surface of the Envelope Protein E1 of Semliki Forest Virus.
      Roussel, A.,Lescar, J.,Vaney, M.,Wengler, G.,Wengler, G.,Rey, F.A.
      (2006) Structure 14: 75
    • The Fusion Glycoprotein Shell of Semliki Forest Virus: An Icosahedral Assembly Primed for Fusogenic Activation at Endosomal Ph.
      Lescar, J.,Roussel, A.,Wien, M.W.,Navaza, J.,Fuller, S.D.,Wengler, G.,Wengler, G.,Rey, F.A.
      (2001) Cell 105: 137
    • Conformational Change and Protein-Protein Interactions of the Fusion Protein of Semliki Forest Virus.
      Gibbons, D.L.,Vaney, M.,Roussel, A.,Vigouroux, A.,Reilly, B.,Lepault, J.,Kielian, M.,Rey, F.A.
      (2004) Nature 427: 320
    • Structure of a Flavivirus Envelope Glycoprotein in its Low-Ph-Induced Membrane Fusion Conformation.
      Bressanelli, S.,Stiasny, K.,Allison, S.L.,Stura, E.A.,Duquerroy, S.,Lescar, J.,Heinz, F.X.,Rey, F.A.
      (2004) Embo J. 23: 728


    Organizational Affiliation

    Institut Pasteur, Département de Virologie, Unité de Virologie Structurale and CNRS URA 3015, F-75724 Paris Cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E1 ENVELOPE GLYCOPROTEIN
A, B, C
473Rubella virus (strain M33)N/A
Find proteins for P08563 (Rubella virus (strain M33))
Go to UniProtKB:  P08563
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NGA
Query on NGA

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A
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 121.680α = 90.00
b = 126.550β = 90.00
c = 130.020γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references