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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF COCKSFOOT MOTTLE VIRUS AT 2.7A RESOLUTION
 
Authors :  K. Tars, A. Zeltins, L. Liljas
Date :  16 Dec 02  (Deposition) - 04 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Sobemovirus, Virus Assembly, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tars, A. Zeltins, L. Liljas
The Three-Dimensional Structure Of Cocksfoot Mottle Virus At 2. 7 A Resolution.
Virology V. 310 287 2003
PubMed-ID: 12781716
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Organism Scientific: COCKSFOOT MOTTLE VIRUS
    Organism Taxid: 40979
    Strain: RUSSIAN 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, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:196 , ASN A:252 , LEU A:253 , ASP C:136 , ASP C:139BINDING SITE FOR RESIDUE CA C 1001
2AC2SOFTWAREASP A:136 , ASP A:139 , LEU B:196 , ASN B:252 , LEU B:253BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREASP B:136 , ASP B:139 , LEU C:196 , ASN C:252 , LEU C:253BINDING SITE FOR RESIDUE CA B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NG0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NG0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NG0)

(-) Exons   (0, 0)

(no "Exon" information available for 1NG0)

(-) 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:192
 aligned with Q9E958_9VIRU | Q9E958 from UniProtKB/TrEMBL  Length:253

    Alignment length:192
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  
         Q9E958_9VIRU    62 DWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
               SCOP domains d1ng0a_ A: Sobemovirus coat protein                                                                                                                                                              SCOP domains
               CATH domains 1ng0A00 A:62-253  [code=2.60.120.20, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author eeeee..eeeeeeeeee.......eeeee.hhhhhhhhhhhh..eeeeeeeeeeeeeee.......eeeeeee.........hhhhhhhh...........hhhhhhh..........eeeee.hhhh....eee.........hhhhhhhh..eeeeeeee......eeeeeeeeeeeeeee...hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ng0 A  62 DWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with Q9E958_9VIRU | Q9E958 from UniProtKB/TrEMBL  Length:253

    Alignment length:192
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  
         Q9E958_9VIRU    62 DWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
               SCOP domains d1ng0b_ B: Sobemovirus coat protein                                                                                                                                                              SCOP domains
               CATH domains 1ng0B00 B:62-253  [code=2.60.120.20, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author eeeee..eeeeeeeeee.......eeeee.hhhhhhhhhhhh..eeeeeeeeeeeeeee.......eeeeeee.........hhhhhhhh...........hhhhhhh..........eeeee.hhhh....eee.........hhhhhhhh..eeeeeeee......eeeeeeeeeeeeeee...hhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ng0 B  62 DWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with Q9E958_9VIRU | Q9E958 from UniProtKB/TrEMBL  Length:253

    Alignment length:218
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
         Q9E958_9VIRU    36 VSRPLNPPAAVGSTLKAGRGRTAGVSDWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
               SCOP domains d1ng0c_ C: Sobemovirus coat protein                                                                                                                                                                                        SCOP domains
               CATH domains 1ng0C00 C:36-253  [code=2.60.120.20, no name defined]                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------------------------Viral_coat-1ng0C01 C:64-248                                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) ----------------------------Viral_coat-1ng0C02 C:64-248                                                                                                                                                              ----- Pfam domains (2)
           Pfam domains (3) ----------------------------Viral_coat-1ng0C03 C:64-248                                                                                                                                                              ----- Pfam domains (3)
         Sec.struct. author ..........eeeeeeee........eeeee..eeeeeeeeee.......eeeee.hhhhhhhhhhhh..eeeeeeeeeeeeeee.......eeeeeee.........hhhhhhhh...........hhhhhhh..........eeeee.hhhh....eee.........hhhhhhhh..eeeeeeee......eeeeeeeeeeeeeee...hhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ng0 C  36 VSRPLNPPAAVGSTLKAGRGRTAGVSDWFDTGMITSYLGGFQRTAGTTDSQVFIVSPAALDRVGTIAKAYALWRPKHWEIVYLPRCSTQTDGSIEMGFLLDYADSVPTNTRTMASSTSFTTSNVWGGGDGSSLLHTSMKSMGNAVTSALPCDEFSNKWFKLSWSTPEESENAHLTDTYVPARFVVRSDFPVVTADQPGHLWLRSRILLKGSVSPSTNL 253
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9E958_9VIRU | Q9E958)
molecular function
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
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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(-) Related Entries Specified in the PDB File

1f2n THE THREE-DIMENSIONAL STRUCTURE OF RICE YELLOW MOTTLE VIRUS
1sbv THE THREE-DIMENSIONAL STRUCTURE OF SOUTHERN BEAN MOSAIC VIRUS RELATED ID: AAA87611 RELATED DB: NCBI THE AMINO ACID SEQUENCE OF COCKSFOOT MOTTLE VIRUS (RUSSIAN ISOLATE).