1JMA

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Herpes simplex virus glycoprotein D bound to the human receptor HveA.

Carfi, A.Willis, S.H.Whitbeck, J.C.Krummenacher, C.Cohen, G.H.Eisenberg, R.J.Wiley, D.C.

(2001) Mol Cell 8: 169-179

  • DOI: https://doi.org/10.1016/s1097-2765(01)00298-2
  • Primary Citation of Related Structures:  
    1JMA, 1L2G

  • PubMed Abstract: 

    Herpes simplex virus (HSV) infection requires binding of the viral envelope glycoprotein D (gD) to cell surface receptors. We report the X-ray structures of a soluble, truncated ectodomain of gD both alone and in complex with the ectodomain of its cellular receptor HveA. Two bound anions suggest possible binding sites for another gD receptor, a 3-O-sulfonated heparan sulfate. Unexpectedly, the structures reveal a V-like immunoglobulin (Ig) fold at the core of gD that is closely related to cellular adhesion molecules and flanked by large N- and C-terminal extensions. The receptor binding segment of gD, an N-terminal hairpin, appears conformationally flexible, suggesting that a conformational change accompanying binding might be part of the viral entry mechanism.


  • Organizational Affiliation

    Department of Medicine, Children's Hospital, Howard Hughes Medical Institute, 320 Longwood Avenue, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HERPESVIRUS ENTRY MEDIATORA [auth B]167Human alphaherpesvirus 1Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92956 (Homo sapiens)
Explore Q92956 
Go to UniProtKB:  Q92956
PHAROS:  Q92956
GTEx:  ENSG00000157873 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92956
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOPROTEIN DB [auth A]290Homo sapiensMutation(s): 0 
UniProt
Find proteins for P57083 (Human herpesvirus 1 (strain Patton))
Explore P57083 
Go to UniProtKB:  P57083
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57083
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.154α = 90
b = 129.154β = 90
c = 80.94γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary