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(-) Description

Title :  STRUCTURE OF HSV-2 GD BOUND TO NECTIN-1
 
Authors :  G. Lu, N. Zhang, J. Qi, Y. Li, Z. Chen, C. Zheng, J. Yan, G. F. Gao
Date :  28 Sep 13  (Deposition) - 01 Oct 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Igv-Like Core, N-/C-Terminal Extensions, Tandem Arranged V-C-C Ig- Like Domains, Receptor Binding, Cell Surface Attachment, Viral, Cellular Surface, Viral Protein-Cell Adhesion Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Lu, N. Zhang, J. Qi, Y. Li, Z. Chen, C. Zheng, G. F. Gao, J. Yan
Crystal Structure Of Hsv-2 Gd Bound To Nectin-1 Reveals A Conserved Mode Of Receptor Recognition.
J. Virol. 2014
PubMed-ID: 25231300  |  Reference-DOI: 10.1128/JVI.01906-14

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN D
    ChainsA, C
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CellHIGH5
    Expression System Cell LineBTI-TN-5B1-4
    Expression System CommonCABBAGE LOOPER
    Expression System PlasmidPFAST-BAC1
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 26-310
    GeneGD, US6
    Organism CommonHHV-2
    Organism ScientificHUMAN HERPESVIRUS 2
    Organism Taxid10313
    Strain333
    SynonymGD
 
Molecule 2 - POLIOVIRUS RECEPTOR-RELATED PROTEIN 1
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 30-335
    GeneHVEC, NECTIN-1, PRR1, PVRL1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHERPES VIRUS ENTRY MEDIATOR C, HERPESVIRUS ENTRY MEDIATOR C, HVEC, HERPESVIRUS IG-LIKE RECEPTOR, HIGR, NECTIN-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:40 , GLN A:41 , ASN A:94 , ASN A:171 , HOH A:610 , HOH A:615 , HOH A:617BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 94 RESIDUES 501 TO 502
2AC2SOFTWAREASN A:121BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 121
3AC3SOFTWAREGLN C:41 , ASN C:94 , ASN C:171 , HOH C:604 , HOH C:605BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 94 RESIDUES 501 TO 502
4AC4SOFTWAREASN C:121 , HOH C:603BINDING SITE FOR MONO-SACCHARIDE NAG C 503 BOUND TO ASN C 121

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:66 -A:189
2A:106 -A:202
3A:118 -A:127
4B:51 -B:124
5B:172 -B:226
6B:269 -B:316
7C:66 -C:189
8C:106 -C:202
9C:118 -C:127
10D:51 -D:124
11D:172 -D:226
12D:269 -D:316

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:243 -Pro A:244
2Ala B:91 -Pro B:92
3Phe B:129 -Pro B:130
4Lys B:178 -Pro B:179
5Asn B:274 -Pro B:275
6Gly B:304 -Pro B:305
7Gly C:243 -Pro C:244
8Ala D:91 -Pro D:92
9Phe D:129 -Pro D:130
10Lys D:178 -Pro D:179
11Asn D:274 -Pro D:275
12Gly D:304 -Pro D:305

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MYW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MYW)

(-) Exons   (0, 0)

(no "Exon" information available for 4MYW)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee...............eeeeeeeeee.....eeee....hhhhhhhh.hhhhhh..eeeeeeeeeee..eeeeeeeeeeeee..........eee..ee......eee......eeee..hhhhheeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhhhh.......ee..hhhhhhhhhhhhhhh...........eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myw A  23 PVLDQLTDPPGVKRVYHIQPSLEDPFQPPSIPITVYYAVLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPYNKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRARASCKYALPLRIPPAACLTSKAYQQGVTVDSIGMLPRFIPENQRTVALYSLKIAGWHGPKPPYTSTLLP 254
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  

Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eee...........eeeeeeeeee.....eeeeeee...eeee.......eee.........eee...hhhhheeeeeeeeee...eeeeeeeeeee...eeeeee....eee.......eeeeeeeeeee....eeeee.....eeeeeeee.....eeeeeeeee.........eeeeeeee..eeeeeeee..eeeeeeeeee............eeeeeeeeee....eeeeee........eee...eeee....hhhhheeeeeeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myw B  33 VQVNDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNITE 335
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   

Chain C from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee...............eeeeeeeeee.....eeeee...hhhhhhhh.hhhhhh.eeeeeeeeeee....eeeeeeeeeeeee.........eee..ee......eee.....eeeee.......eeeeeeeee..eeeeeeeeeee..............hhhhh.hhhhhhhhh.......ee....hhhhhhhhhhhhh...........ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myw C  23 PVLDQLTDPPGVKRVYHIQPSLEDPFQPPSIPITVYYAVLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPYNKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRARASCKYALPLRIPPAACLTSKAYQQGVTVDSIGMLPRFIPENQRTVALYSLKIAGWHGPKPPYTSTLLP 254
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  

Chain D from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eee...........eeeeeeeeee......eeeeee...eeee...................eee...hhhhheeeeeeeeee.....ee..eeeee...eeeeee....ee........eeeeeeeeeee....eeeeee....eeeeeeee.....eeeeeeeee..hhhhh..eeeeeeee..eeeeeeee..eeeeeeeeee............eeeeeeeeee....eeeeee........eee...eeee....hhhhheeeeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4myw D  33 VQVNDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNITE 335
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   

   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  (0, 0)

(no "SCOP Domain" information available for 4MYW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MYW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MYW)

(-) Gene Ontology  (50, 54)

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  Cis Peptide Bonds
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    Lys B:178 - Pro B:179   [ RasMol ]  
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 Related Entries

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        GD_HHV23 | P031724myv
        NECT1_HUMAN | Q152233alp 3sku 3u82 3u83 4fmf

(-) Related Entries Specified in the PDB File

3u82 STRUCTURE OF HSV-1 GD BOUND TO NECTIN-1
4myv FREE HSV-2 GD STRUCTURE