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(-) Description

Title :  STRUCTURE OF THE LARGE PROTEASE RESISTANT UPPER DOMAIN OF VP5, THE MAJOR CAPSID PROTEIN OF HERPES SIMPLEX VIRUS-1
 
Authors :  B. R. Bowman, M. L. Baker, F. J. Rixon, W. Chiu, F. A. Quiocho
Date :  15 Jan 03  (Deposition) - 20 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Novel Fold, Alpha Plus Beta, Viral Capsid Protein, Folding Nucleus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Bowman, M. L. Baker, F. J. Rixon, W. Chiu, F. A. Quiocho
Structure Of The Herpesvirus Major Capsid Protein
Embo J. V. 22 757 2003
PubMed-ID: 12574112  |  Reference-DOI: 10.1093/EMBOJ/CDG086
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VP5 UPPER DOMAIN
    Gene: UL19
    Organism Common: HERPES SIMPLEX VIRUS TYPE 1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Synonym: CAPSID PROTEIN VP5

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NO7)

(-) Sites  (0, 0)

(no "Site" information available for 1NO7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NO7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NO7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NO7)

(-) Exons   (0, 0)

(no "Exon" information available for 1NO7)

(-) 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:542
 aligned with MCP_HHV11 | P06491 from UniProtKB/Swiss-Prot  Length:1374

    Alignment length:562
                                   493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043  
           MCP_HHV11    484 ANPYGAYVAAPAGPAADMQQLFLNAWGQRLAHGRVRWVAEGQMTPEQFMQPDNANLALELHPAFDFFVGVADVELPGGDVPPAGPGEIQATWRVVNGNLPLALCPAAFRDARGLELGVGRHAMAPATIAAVRGAFDDRNYPAVFYLLQAAIHGSEHVFCALARLVVQCITSYWNNTRCAAFVNDYSLVSYVVTYLGGDLPEECMAVYRDLVAHVEALAQLVDDFTLTGPELGGQAQAELNHLMRDPALLPPLVWDCDALMRRAALDRHRDCRVSAGGHDPVYAAACNVATADFNRNDGQLLHNTQARAADAADDRPHRGADWTVHHKIYYYVMVPAFSRGRCCTAGVRFDRVYATLQNMVVPEIAPGEECPSDPVTDPAHPLHPANLVANTVNAMFHNGRVVVDGPAMLTLQVLAHNMAERTTALLCSAAPDAGANTASTTNMRIFDGALHAGILLMAPQHLDHTIQNGDYFYPLPVHALFAGADHVANAPNFPPALRDLSRQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFKISPVALHHQLKTGLH 1045
               SCOP domains d1no7a_ A: Major capsid protein VP5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......hhhhhhhhhhh.hhhhhhh.......-----------------........eee.....................eee...hhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..............hhhhhhhhh.........ee.....eee...............eee.................hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.........................hhhhh...hhhhhhhhh....hhhhhhhhhhhhh.......eeeeee.........---...eeeeee..eeee...............eee........hhhhhhh.......hhhhhh.....hhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1no7 A  484 ANPYGAYVAAPAGPAADMQQLFLNAWGQRLAHGRVRWVA-----------------ALELHPAFDFFVGVADVELPGGDVPPAGPGEIQATWRVVNGNLPLALCPAAFRDARGLELGVGRHAMAPATIAAVRGAFDDRNYPAVFYLLQAAIHGSEHVFCALARLVVQCITSYWNNTRCAAFVNDYSLVSYVVTYLGGDLPEECMAVYRDLVAHVEALAQLVDDFTLTGPELGGQAQAELNHLMRDPALLPPLVWDCDALMRRAALDRHRDCRVSAGGHDPVYAAACNVATADFNRNDGQLLHNTQARAADAADDRPHRGADWTVHHKIYYYVMVPAFSRGRCCTAGVRFDRVYATLQNMVVPEIAPGEECPSDPVTDPAHPLHPANLVANTVNAMFHNGRVVVDGPAMLTLQVLAHNMAERTTALLCSAAPDAGANTA---NMRIFDGALHAGILLMAPQHLDHTIQNGDYFYPLPVHALFAGADHVANAPNFPPALRDLSRQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFKISPVALHHQLKTGLH 1045
                                   493       503       513        |-         -      |543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       | - |     933       943       953       963       973       983       993      1003      1013      1023      1033      1043  
                                                                522               540                                                                                                                                                                                                                                                                                                                                                                                          921 925                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:534
 aligned with MCP_HHV11 | P06491 from UniProtKB/Swiss-Prot  Length:1374

    Alignment length:562
                                   493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043  
           MCP_HHV11    484 ANPYGAYVAAPAGPAADMQQLFLNAWGQRLAHGRVRWVAEGQMTPEQFMQPDNANLALELHPAFDFFVGVADVELPGGDVPPAGPGEIQATWRVVNGNLPLALCPAAFRDARGLELGVGRHAMAPATIAAVRGAFDDRNYPAVFYLLQAAIHGSEHVFCALARLVVQCITSYWNNTRCAAFVNDYSLVSYVVTYLGGDLPEECMAVYRDLVAHVEALAQLVDDFTLTGPELGGQAQAELNHLMRDPALLPPLVWDCDALMRRAALDRHRDCRVSAGGHDPVYAAACNVATADFNRNDGQLLHNTQARAADAADDRPHRGADWTVHHKIYYYVMVPAFSRGRCCTAGVRFDRVYATLQNMVVPEIAPGEECPSDPVTDPAHPLHPANLVANTVNAMFHNGRVVVDGPAMLTLQVLAHNMAERTTALLCSAAPDAGANTASTTNMRIFDGALHAGILLMAPQHLDHTIQNGDYFYPLPVHALFAGADHVANAPNFPPALRDLSRQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFKISPVALHHQLKTGLH 1045
               SCOP domains d1no7b_ B: Major capsid protein VP5                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Herpes_MCP-1no7B01 B:484-1045                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) Herpes_MCP-1no7B02 B:484-1045                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..hhhhh......hhhhhhhhhhh.hhhhhhh.......----------------.........eee.....................eee...hhhhh.....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..............hhhhhhhhh.........ee.....eee...............eee.................hhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.........................hhhhh...hhhhhhhhh....hhhhhhhhhhhhh.......eeeeee.....--..---...eeeeee..eeee.....-------...eee........hhhhhhh.......hhhhhh.....hhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1no7 B  484 ANPYGAYVAAPAGPAADMQQLFLNAWGQRLAHGRVRWVA----------------LALELHPAFDFFVGVADVELPGGDVPPAGPGEIQATWRVVNGNLPLALCPAAFRDARGLELGVGRHAMAPATIAAVRGAFDDRNYPAVFYLLQAAIHGSEHVFCALARLVVQCITSYWNNTRCAAFVNDYSLVSYVVTYLGGDLPEECMAVYRDLVAHVEALAQLVDDFTLTGPELGGQAQAELNHLMRDPALLPPLVWDCDALMRRAALDRHRDCRVSAGGHDPVYAAACNVATADFNRNDGQLLHNTQARAADAADDRPHRGADWTVHHKIYYYVMVPAFSRGRCCTAGVRFDRVYATLQNMVVPEIAPGEECPSDPVTDPAHPLHPANLVANTVNAMFHNGRVVVDGPAMLTLQVLAHNMAERTTALLCSAAPDAG--TA---NMRIFDGALHAGILLMAPQH-------GDYFYPLPVHALFAGADHVANAPNFPPALRDLSRQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFKISPVALHHQLKTGLH 1045
                                   493       503       513        |-         -     | 543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913   |  || - |     933       943|      953       963       973       983       993      1003      1013      1023      1033      1043  
                                                                522              539                                                                                                                                                                                                                                                                                                                                                                                       917  || 925                944     952                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              920|                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               921
   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
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1NO7)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Herpes_MCP] (1)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCP_HHV11 | P06491)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0039622    T=16 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=16 symmetry. The T=16 capsid is composed of 12 pentameric and 150 hexameric capsomeres.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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