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PDBsum entry 2h6o

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protein ligands links
Viral protein PDB id
2h6o
Jmol
Contents
Protein chain
440 a.a.
Ligands
NAG-NAG-MAN-MAN-
BMA-MAN-MAN
NAG-NAG-MAN-BMA-
MAN-MAN-MAN
NDG-NAG-MAN-MAN-
MAN-MAN-MAN-MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN-
MAN
NAG-NAG-MAN-MAN-
MAN-MAN-MAN-MAN-
GAL-GAL
NAG-NAG-MAN-MAN-
MAN-MAN-MAN-GAL-
GAL
NAG-NAG-MAN-BMA-
MAN-MAN-MAN-MAN-
MAN-GAL-GAL
NAG-NAG-MAN ×2
NAG-NAG-MAN-MAN-
MAN
NAG-NAG-MAN-MAN-
MAN-MAN-MAN-BMA
NAG-NDG-MAN-MAN-
MAN-MAN-MAN-NAG-
FUC
NAG-NDG-MAN-MAN-
MAN-NAG-BMA-FUC-
MAN-MAN
NAG-NAG
PDB id:
2h6o
Name: Viral protein
Title: Epstein barr virus major envelope glycoprotein
Structure: Major outer envelope glycoprotein gp350. Chain: a. Fragment: extracellular fragment. Engineered: yes
Source: Human herpesvirus 4. Epstein-barr virus. Organism_taxid: 10376. Strain: gd1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108
Resolution:
3.50Å     R-factor:   0.326     R-free:   0.368
Authors: X.S.Chen
Key ref:
G.Szakonyi et al. (2006). Structure of the Epstein-Barr virus major envelope glycoprotein. Nat Struct Mol Biol, 13, 996. PubMed id: 17072314 DOI: 10.1038/nsmb1161
Date:
31-May-06     Release date:   31-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9QP87  (Q9QP87_EBVG) -  Major outer envelope glycoprotein gp350
Seq:
Struc:
 
Seq:
Struc:
886 a.a.
440 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   1 term 
  Biological process     viral infectious cycle   1 term 

 

 
DOI no: 10.1038/nsmb1161 Nat Struct Mol Biol 13:996 (2006)
PubMed id: 17072314  
 
 
Structure of the Epstein-Barr virus major envelope glycoprotein.
G.Szakonyi, M.G.Klein, J.P.Hannan, K.A.Young, R.Z.Ma, R.Asokan, V.M.Holers, X.S.Chen.
 
  ABSTRACT  
 
Epstein-Barr virus (EBV) infection of B cells is associated with lymphoma and other human cancers. EBV infection is initiated by the binding of the viral envelope glycoprotein (gp350) to the cell surface receptor CR2. We determined the X-ray structure of the highly glycosylated gp350 and defined the CR2 binding site on gp350. Polyglycans shield all but one surface of the gp350 polypeptide, and we demonstrate that this glycan-free surface is the receptor-binding site. Deglycosylated gp350 bound CR2 similarly to the glycosylated form, suggesting that glycosylation is not important for receptor binding. Structure-guided mutagenesis of the glycan-free surface disrupted receptor binding as well as binding by a gp350 monoclonal antibody, a known inhibitor of virus-receptor interactions. These results provide structural information for developing drugs and vaccines to prevent infection by EBV and related viruses.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The various polyglycan chain conformations on the protein surface. Polyglycans are shown as sticks and polypeptide as ribbon. (a) Overall gp350 structure with the 14 polyglycan chains on the surface. (b) A portion of the electron density map corresponding to a polyglycan. (c) The polyglycan chain on Asn345 lying parallel to the protein surface, docking its residues on the protein surface. (d) Two polyglycan chains (from Asn45 and Asn114) interacting with each other over a long distance through their distal residues. (e) The polyglycan chain on Asn277 projecting out from the protein surface. This type of polyglycan is stabilized by crystal contacts.
Figure 3.
Figure 3. Protein surface features of glycosylated gp350 and its receptor, CR2. (a) Full view of glycosylated gp350, showing extensive coverage of the protein (ribbons) by the 14 polyglycans (molecular surface). Arrow marks the glycan-free surface on the protein. (b) Surface representation of glycosylated gp350 in the same orientation as in a, colored by charge (red, negatively charged residues; blue, positive; white, neutral) to show a highly negatively charged area on the glycan-free protein surface (arrow and circle). (c) Surface charge features of the SCR1-SCR2 domain of CR2, which binds gp350, showing a highly positively charged surface, in contrast to the negatively charged surface in b. There are a total of 12 charged residues (arginines and lysines) on this side of the surface, compared with 2 on the opposite side (see d). (d) The CR2 surface opposite that in c, which is mostly neutral.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 996-0) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21478902 S.A.Connolly, J.O.Jackson, T.S.Jardetzky, and R.Longnecker (2011).
Fusing structure and function: a structural view of the herpesvirus entry machinery.
  Nat Rev Microbiol, 9, 369-381.  
19889766 C.Busse, R.Feederle, M.Schnölzer, U.Behrends, J.Mautner, and H.J.Delecluse (2010).
Epstein-Barr viruses that express a CD21 antibody provide evidence that gp350's functions extend beyond B-cell surface binding.
  J Virol, 84, 1139-1147.  
21067549 J.Söllner, A.Heinzel, G.Summer, R.Fechete, L.Stipkovits, S.Szathmary, and B.Mayer (2010).
Concept and application of a computational vaccinology workflow.
  Immunome Res, 6, S7.  
20004209 P.J.Coombs, R.Harrison, S.Pemberton, A.Quintero-Martinez, S.Parry, S.M.Haslam, A.Dell, M.E.Taylor, and K.Drickamer (2010).
Identification of novel contributions to high-affinity glycoprotein-receptor interactions using engineered ligands.
  J Mol Biol, 396, 685-696.  
19153826 A.Kawaguchi, K.Kanai, Y.Satoh, C.Touge, K.Nagata, T.Sairenji, and Y.Inoue (2009).
The evolution of Epstein-Barr virus inferred from the conservation and mutation of the virus glycoprotein gp350/220 gene.
  Virus Genes, 38, 215-223.  
18420792 A.D.Gu, Y.B.Xie, H.Y.Mo, W.H.Jia, M.Y.Li, M.Li, L.Z.Chen, Q.S.Feng, Q.Liu, C.N.Qian, and Y.X.Zeng (2008).
Antibodies against Epstein-Barr virus gp78 antigen: a novel marker for serological diagnosis of nasopharyngeal carcinoma detected by xMAP technology.
  J Gen Virol, 89, 1152-1158.  
18615077 J.E.Lee, M.L.Fusco, A.J.Hessell, W.B.Oswald, D.R.Burton, and E.O.Saphire (2008).
Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor.
  Nature, 454, 177-182.
PDB code: 3csy
18786993 K.A.Young, A.P.Herbert, P.N.Barlow, V.M.Holers, and J.P.Hannan (2008).
Molecular basis of the interaction between complement receptor type 2 (CR2/CD21) and Epstein-Barr virus glycoprotein gp350.
  J Virol, 82, 11217-11227.  
17925391 K.A.Young, X.S.Chen, V.M.Holers, and J.P.Hannan (2007).
Isolating the Epstein-Barr virus gp350/220 binding site on complement receptor type 2 (CR2/CD21).
  J Biol Chem, 282, 36614-36625.  
17459936 L.M.Hutt-Fletcher (2007).
Epstein-Barr virus entry.
  J Virol, 81, 7825-7832.  
17473875 M.Crispin, D.I.Stuart, and E.Y.Jones (2007).
Building meaningful models of glycoproteins.
  Nat Struct Mol Biol, 14, 354; discussion 354-354; discussion 355.  
17473874 , (0).
  , (), 0.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.