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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE HSV-1 GE ECTODOMAIN
 
Authors :  E. R. Sprague, C. Wang, D. Baker, P. J. Bjorkman
Date :  29 Mar 06  (Deposition) - 30 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Fc Receptor, Ig V Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Sprague, C. Wang, D. Baker, P. J. Bjorkman
Crystal Structure Of The Hsv-1 Fc Receptor Bound To Fc Reveals A Mechanism For Antibody Bipolar Bridging.
Plos Biol. V. 4 1 2006
PubMed-ID: 16646632  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0040148

(-) Compounds

Molecule 1 - GLYCOPROTEIN E
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: C-TERMINAL DOMAIN OF THE GE ECTODOMAIN
    Gene: GE, US8
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10306
    Strain: KOS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2GIY)

(-) Sites  (0, 0)

(no "Site" information available for 2GIY)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:297
2A:280 -A:289
3A:314 -A:323
4B:271 -B:297
5B:280 -B:289
6B:314 -B:323

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GIY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GE_HHV11_004 *T239AGE_HHV11  ---  ---A/BT239A
2UniProtVAR_GE_HHV11_005 *S257AGE_HHV11  ---  ---A/BS257A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GIY)

(-) Exons   (0, 0)

(no "Exon" information available for 2GIY)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:179
 aligned with GE_HHV11 | P04488 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:179
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
             GE_HHV11   218 HVRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLPQRGAD 396
               SCOP domains d2giya1 A:218-394 Alphaherpesvirus glycoprotein E                                                                                                                                -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eee......ee...eeeeee.....eeeeeeeeee........eeeehhhhhh..hhhhhh......ee.......eeeeeeee....hhhhheeeeee.....eee......eee...hhhhheeeeeeeee..eeeeeeeeeee.......eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------A-----------------A------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2giy A 218 HVRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLDIEGRG 396
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         


Chain A from PDB  Type:PROTEIN  Length:179
 aligned with Q703E9_HHV1 | Q703E9 from UniProtKB/TrEMBL  Length:550

    Alignment length:179
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         
          Q703E9_HHV1   218 HVRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLPQRGAD 396
               SCOP domains d2giya1 A:218-394 Alphaherpesvirus glycoprotein E                                                                                                                                -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eee......ee...eeeeee.....eeeeeeeeee........eeeehhhhhh..hhhhhh......ee.......eeeeeeee....hhhhheeeeee.....eee......eee...hhhhheeeeeeeee..eeeeeeeeeee.......eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------A-----------------A------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2giy A 218 HVRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLDIEGRG 396
                                   227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387         


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with GE_HHV11 | P04488 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:178
                                   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
             GE_HHV11   219 VRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLPQRGAD 396
               SCOP domains d2giyb_ B: Alphaherpesvirus glycoprotein E                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eee......ee...eeeeee.....eeeeeeeeee.......eeeeehhhhhh..hhhhhh..hhh.ee.......eeeeeeee.........eeeeee.....ee........ee...hhhhheeeeeeeee..eeeeeeeeeee......eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------A-----------------A------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2giy B 219 VRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLDIEGRG 396
                                   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with Q703E9_HHV1 | Q703E9 from UniProtKB/TrEMBL  Length:550

    Alignment length:178
                                   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388        
          Q703E9_HHV1   219 VRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLPQRGAD 396
               SCOP domains d2giyb_ B: Alphaherpesvirus glycoprotein E                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eee......ee...eeeeee.....eeeeeeeeee.......eeeeehhhhhh..hhhhhh..hhh.ee.......eeeeeeee.........eeeeee.....ee........ee...hhhhheeeeeeeee..eeeeeeeeeee......eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------A-----------------A------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2giy B 219 VRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLDIEGRG 396
                                   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GIY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GIY)

(-) Gene Ontology  (14, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GE_HHV11 | P04488)
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0044177    host cell Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic host cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
    GO:0044178    host cell Golgi membrane    The lipid bilayer surrounding any of the compartments of the host cell Golgi apparatus.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0044156    host cell junction    A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain A,B   (Q703E9_HHV1 | Q703E9)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GE_HHV11 | P04488: 2gj7

(-) Related Entries Specified in the PDB File

2gjy MODEL OF THE C-TERMINAL DOMAIN OF THE GE ECTODOMAIN BOUND TO FC DERIVED FROM CRYSTALLOGRAPHIC ANALYSIS OF GE-GI/FC CRYSTALS