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(-) Description

Title :  STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR-MEDIATED ACTIVATION OF VIRUS ENTRY
 
Authors :  C. Krummenacher, V. M. Supekar, J. C. Whitbeck, E. Lazear, S. A. Connolly, R. J. Eisenberg, G. H. Cohen, D. C. Wiley, A. Carfi
Date :  05 Oct 05  (Deposition) - 21 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Virus, Herpes Simplex Virus, Hsv-1, Glycoprotein D, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Krummenacher, V. M. Supekar, J. C. Whitbeck, E. Lazear, S. A. Connolly, R. J. Eisenberg, G. H. Cohen, D. C. Wiley, A. Carfi
Structure Of Unliganded Hsv Gd Reveals A Mechanism For Receptor-Mediated Activation Of Virus Entry.
Embo J. V. 24 4144 2005
PubMed-ID: 16292345  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600875

(-) Compounds

Molecule 1 - GLYCOPROTEIN D
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PDL485
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Mutation: YES
    Organism Common: HUMAN HERPES SIMPLEX VIRUS 1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: N-ACETYL-D-GLUCOSAMINE LINKED TO ASN94 FOR BOTH CHAINS A AND B
    Strain: PATTON

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN5Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:41 , PRO A:92 , ASN A:94 , ASN A:171 , NAG A:1308BINDING SITE FOR RESIDUE NAG A1307
02AC2SOFTWARENAG A:1307BINDING SITE FOR RESIDUE NAG A1308
03AC3SOFTWAREGLN B:41 , PRO B:92 , ASN B:94 , ASN B:171 , NAG B:1309BINDING SITE FOR RESIDUE NAG B1308
04AC4SOFTWARENAG B:1308BINDING SITE FOR RESIDUE NAG B1309
05AC5SOFTWAREGLN A:27 , PHE A:223 , ILE A:224 , ASN A:227 , PRO A:297BINDING SITE FOR RESIDUE CL A1309
06AC6SOFTWAREGLU A:146 , GLU A:226BINDING SITE FOR RESIDUE ZN A1310
07AC7SOFTWAREGLN B:27 , PHE B:223 , ILE B:224 , ASN B:227BINDING SITE FOR RESIDUE CL B1310
08AC8SOFTWAREGLU B:146 , GLU B:226 , ARG B:229BINDING SITE FOR RESIDUE NA B1311
09AC9SOFTWARESER B:68 , TRP B:241 , LYS B:245 , HOH B:2028BINDING SITE FOR RESIDUE NA B1312
10BC1SOFTWAREASP B:147 , ASP B:281BINDING SITE FOR RESIDUE ZN B1313
11BC2SOFTWAREASP A:301 , HIS B:39 , ASP B:215BINDING SITE FOR RESIDUE ZN B1314
12BC3SOFTWAREHIS A:39 , ASP A:215 , ASP B:301 , HOH B:2035BINDING SITE FOR RESIDUE ZN B1315
13BC4SOFTWAREHIS B:242 , ASP B:272BINDING SITE FOR RESIDUE ZN B1316

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:37 -A:302
2A:66 -A:189
3A:106 -A:202
4A:118 -A:127
5B:37 -B:302
6B:66 -B:189
7B:106 -B:202
8B:118 -B:127

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:243 -Pro A:244
2Gly B:243 -Pro B:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C3A)

(-) Exons   (0, 0)

(no "Exon" information available for 2C3A)

(-) 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:253
 aligned with GD_HHV1P | P57083 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:283
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
             GD_HHV1P    49 VLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPY 331
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..................eeeeeee.....eeee....hhhhhhhh...hhhhh.eeeeeeeeeee..eeeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhhh........ee.....hhhhhhhhhhhhh..........ee....------------------------------..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c3a A  24 VLDQLTDPPGVRRCYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPP------------------------------VAPQIPPNWHIPSIQDCATPY 306
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253 |       -         -         -  |    293       303   
                                                                                                                                                                                                                                                                 255                            286                    


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with GD_HHV1P | P57083 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:286
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326      
             GD_HHV1P    47 LPVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDAATPYH 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2c3aB00 B:22-307  [code=2.70.230.10, no name defined]                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..................eeeeeee.....eeee....hhhhh......hhhhh.eeeeeeeeee....eeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhh.........ee..hhhhhhhhhhhhhhhh..................------------...................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c3a B  22 LPVLDQLTDPPGVRRCYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPEL------------PEDPEDSALLEDPVGTVAPQIPPNWHIPSIQDCATPYH 307
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     |   -       271       281       291       301      
                                                                                                                                                                                                                                                                     257          270
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 2C3A)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C3A)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GD_HHV1P | P57083)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GD_HHV1P | P57083: 1jma 1l2g 2c36

(-) Related Entries Specified in the PDB File

1jma CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIND BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
1l2g STRUCTURE OF A C-TERMINALLY TRUNCATED FORM OF GLYCOPROTEIND FROM HSV-1
2c36 STRUCTURE OF UNLIGANDED HSV GD REVEALS A MECHANISM FOR RECEPTOR-MEDIATED ACTIVATION OF VIRUS ENTRY