4ADI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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This is version 1.2 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:  
    4ADG, 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 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 ...

    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: 
    • 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
    • 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
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E1 ENVELOPE GLYCOPROTEINA, B, C473Rubella virusMutation(s): 0 
UniProt
Find proteins for P08563 (Rubella virus (strain M33))
Explore P08563 
Go to UniProtKB:  P08563
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA (Subject of Investigation/LOI)
Query on NGA

Download Ideal Coordinates CCD File 
CA [auth B], DA [auth B], P [auth A], Q [auth A], QA [auth C], RA [auth C]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth B], D [auth A], EA [auth C], O [auth A], PA [auth C], R [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth B], N [auth A], NA [auth C], OA [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , FA [auth C] , G [auth A] , GA [auth C] , H [auth A] , HA [auth C] , I [auth A] , 
E [auth A], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], KA [auth C], S [auth B], T [auth B], U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], MA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth A], LA [auth C], V [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.98α = 90
b = 121.38β = 90
c = 126.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary