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(-) Description

Title :  TOBACCO NECROSIS VIRUS
 
Authors :  Y. Oda, K. Fukuyama
Date :  20 May 00  (Deposition) - 30 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Virus, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Oda, K. Saeki, Y. Takahashi, T. Maeda, H. Naitow, T. Tsukihara, K. Fukuyama
Crystal Structure Of Tobacco Necrosis Virus At 2. 25 A Resolution.
J. Mol. Biol. V. 300 153 2000
PubMed-ID: 10864506  |  Reference-DOI: 10.1006/JMBI.2000.3831
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Organism Scientific: UNIDENTIFIED TOBACCO NECROSIS VIRUS
    Organism Taxid: 12054
    Other Details: THIS STRAIN IS CLOSE TO STRAIN A.
    Strain: TOYAMA ISOLATE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:173 , GLN C:174 , THR C:175BINDING SITE FOR RESIDUE CA C 301
2AC2SOFTWAREASP B:160 , ASP B:163 , THR C:219 , ASN C:275BINDING SITE FOR RESIDUE CA B 302
3AC3SOFTWARETHR A:219 , ASN A:275 , HOH A:841 , ASP C:160 , ASP C:163BINDING SITE FOR RESIDUE CA A 303
4AC4SOFTWAREASP A:160 , ASP A:163 , THR B:219 , ASN B:275BINDING SITE FOR RESIDUE CA B 304
5AC5SOFTWARESER A:173 , GLN A:174 , THR A:175BINDING SITE FOR RESIDUE CA A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C8N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C8N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C8N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C8N)

(-) Exons   (0, 0)

(no "Exon" information available for 1C8N)

(-) 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:189
 aligned with Q9IPS9_9TOMB | Q9IPS9 from UniProtKB/TrEMBL  Length:269

    Alignment length:189
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         
         Q9IPS9_9TOMB    80 NSTVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMN 268
               SCOP domains d1c8na_ A: Necrovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1c8nA00 A:87-275  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee........eeeeee.....hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhhh...eee....hhhhhhhhh.........eee.hhhhh....ee..hhhhhhh.hhhhhhh....eeeeeee.........eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8n A  87 NSTVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMN 275
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266         


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with Q9IPS9_9TOMB | Q9IPS9 from UniProtKB/TrEMBL  Length:269

    Alignment length:189
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
         Q9IPS9_9TOMB    81 STVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMNV 269
               SCOP domains d1c8nb_ B: Necrovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1c8nB00 B:88-276  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee........eeeeee.....hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhh....eee.......hhhhhh.........eee.hhhhh....ee..hhhhhhh.hhhhhhhhh..eeeeeee.........eeeeeeeeeeeeee.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8n B  88 STVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMNV 276
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267         


Chain C from PDB  Type:PROTEIN  Length:219
 aligned with Q9IPS9_9TOMB | Q9IPS9 from UniProtKB/TrEMBL  Length:269

    Alignment length:219
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259         
         Q9IPS9_9TOMB    50 GVSRAGGFVTAPVIGAMVTRPTVPRFGMRGNSTVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMN 268
               SCOP domains d1c8nc_ C: Necrovirus coat protein                                                                                                                                                                                          SCOP domains
               CATH domains 1c8nC00 C:57-275  [code=2.60.120.20, no name defined]                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..................eeeee..eeeeeeeeeeee........eeeeee.....hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhhh...eee....hhhhhhhhhh........eee.hhhhh....ee..hhhhhhh.hhhhhh.....eeeeeee.........eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8n C  57 GVSRAGGFVTAPVIGAMVTRPTVPRFGMRGNSTVVSNSELILNLTPIALAYTVQSLPLIATQPAWLGTIADNYSKWRWVSLRIIYSPKCPTTTSGTVAMCLSYDRNDVAPGSRVQLSQTYKAINFPPYAGYDGAAILNTDVTPTSAIYVDVDVTRFDKAWYSTIGTAAFAALTAFDQNQFCPCTVHIGSDGGPAVAVPPGDIFFKYVIELIEPINPTMN 275
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C8N)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9IPS9_9TOMB | Q9IPS9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

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