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(-) Description

Title :  CRYSTAL STRUCTURE OF EPSTEIN-BARR VIRUS GP42 PROTEIN
 
Authors :  A. Kirschner, T. Jardetzky
Date :  24 Nov 08  (Deposition) - 23 Jun 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  C Type Lectin, Herpesvirus, Virus Entry, Membrane Fusion, Host-Virus Interaction, Lectin, Membrane, Transmembrane, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Kirschner, J. Sorem, R. Longnecker, T. S. Jardetzky
Structure Of Epstein-Barr Virus Glycoprotein 42 Suggests A Mechanism For Triggering Receptor-Activated Virus Entry.
Structure V. 17 223 2009
PubMed-ID: 19217393  |  Reference-DOI: 10.1016/J.STR.2008.12.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOPROTEIN GP42
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPBACGUS-3
    Expression System Taxid7108
    GeneBZLF2
    Organism ScientificHUMAN HERPESVIRUS 4 (STRAIN B95-8)
    Organism Taxid10377
    StrainB95-8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A 
Biological Unit 3 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3FD4)

(-) Sites  (0, 0)

(no "Site" information available for 3FD4)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:99 -A:138
2A:102 -A:115
3A:128 -A:214
4A:132 -A:216
5A:192 -A:208
6B:99 -B:138
7B:102 -B:115
8B:128 -B:214
9B:132 -B:216
10B:192 -B:208

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FD4)

(-) Exons   (0, 0)

(no "Exon" information available for 3FD4)

(-) Sequences/Alignments

Asymmetric 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:140
 aligned with GP42_EBVB9 | P03205 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:140
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222
           GP42_EBVB9    83 PTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSN 222
               SCOP domains d3fd4a_ A: automated matches                                                                                                                 SCOP domains
               CATH domains 3fd4A00 A:83-222 Mannose-Binding Protein A, subunit A                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................eee..eeeee.......hhhhhhhhhhh..eee......hhhhhhh......eeee..ee.....eee..eeee..........eeee......ee..........eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fd4 A  83 PTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSN 222
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with GP42_EBVB9 | P03205 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:147
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       
           GP42_EBVB9    76 VKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSN 222
               SCOP domains d3fd4b_ B: automated matches                                                                                                                        SCOP domains
               CATH domains 3fd4B00 B:76-222 Mannose-Binding Protein A, subunit A                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................eee..eeeee.......hhhhhhhhhhh..eee......hhhhhhh......eeee..ee.....ee.................eeee......ee..........eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fd4 B  76 VKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSN 222
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FD4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GP42_EBVB9 | P03205)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    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: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: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:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GP42_EBVB9 | P032051kg0

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