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(-) Description

Title :  COWPEA MOSAIC VIRUS (CPMV)
 
Authors :  T. Lin, Z. Chen, R. Usha, C. V. Stauffacher, J. -B. Dai, T. Schmidt, J. E. J
Date :  11 Feb 03  (Deposition) - 18 Mar 03  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  1,2
Biol. Unit 1:  1,2  (60x)
Keywords :  Comovirus, Virus, Viral Coat Protein, Cowpea Mosaic Virus (Cpmv), Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lin, Z. Chen, R. Usha, C. V. Stauffacher, J. -B. Dai, T. Schmidt, J. E. Johnson
The Refined Crystal Structure Of Cowpea Mosaic Virus At 2. 8 Resolution
Virology V. 265 20 1999
PubMed-ID: 10603314  |  Reference-DOI: 10.1006/VIRO.1999.0038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
    Chains: 1
    Organism Scientific: COWPEA MOSAIC VIRUS
    Organism Taxid: 12264
    Synonym: CPMV, GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37
 
Molecule 2 - COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
    Chains: 2
    Organism Scientific: COWPEA MOSAIC VIRUS
    Organism Taxid: 12264
    Synonym: CPMV, GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : 12
Biological Unit 1 (60x): 12

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NY7)

(-) Sites  (0, 0)

(no "Site" information available for 1NY7)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
12:187 -2:355

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala 1:22 -Pro 1:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NY7)

(-) Exons   (0, 0)

(no "Exon" information available for 1NY7)

(-) 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 1 from PDB  Type:PROTEIN  Length:189
 aligned with POL2_CPMVS | P03599 from UniProtKB/Swiss-Prot  Length:1046

    Alignment length:189
                                   843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013         
          POL2_CPMVS    834 GPVCAEASDVYSPCMIASTPPAPFSDVTAVTFDLINGKITPVGDDNWNTHIYNPPIMNVLRTAAWKSGTIHVQLNVRGAGVKRADWDGQVFVYLRQSMNPESYDARTFVISQPGSAMLNFSFDIIGPNSGFEFAESPWANQTTWYLECVATNPRQIQQFEVNMRFDPNFRVAGNILMPPFPLSTETPPL 1022
               SCOP domains d1ny711 1:1-189 Comovirus coat proteins (VP37 and VP23)                                                                                                                                       SCOP domains
               CATH domains 1ny7100 1:1-189  [code=2.60.120.20, no name defined]                                                                                                                                          CATH domains
               Pfam domains ---Como_SCP-1ny7101 1:4-183                                                                                                                                                            ------ Pfam domains
         Sec.struct. author ...........eeeeeee.........eeeeee....eeee......eeee..hhhhhhhhheeeeeeeeeeeeeeee...hhhhh...eeeeee..........eeeee.....eeeeeeeee....................eeeeee.....eeeeeeeeee....eeeeeee...ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ny7 1    1 GPVCAEASDVYSPCMIASTPPAPFSDVTAVTFDLINGKITPVGDDNWNTHIYNPPIMNVLRTAAWKSGTIHVQLNVRGAGVKRADWDGQVFVYLRQSMNPESYDARTFVISQPGSAMLNFSFDIIGPNSGFEFAESPWANQTTWYLECVATNPRQIQQFEVNMRFDPNFRVAGNILMPPFPLSTETPPL  189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain 2 from PDB  Type:PROTEIN  Length:369
 aligned with POL2_CPMVS | P03599 from UniProtKB/Swiss-Prot  Length:1046

    Alignment length:369
                                   469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819         
          POL2_CPMVS    460 MEQNLFALSLDDTSSVRGSLLDTKFAQTRVLLSKAMAGGDVLLDEYLYDVVNGQDFRATVAFLRTHVITGKIKVTATTNISDNSGCCLMLAINSGVRGKYSTDVYTICSQDSMTWNPGCKKNFSFTFNPNPCGDSWSAEMISRSRVRMTVICVSGWTLSPTTDVIAKLDWSIVNEKCEPTIYHLADCQNWLPLNRWMGKLTFPQGVTSEVRRMPLSIGGGAGATQAFLANMPNSWISMWRYFRGELHFEVTKMSSPYIKATVTFLIAFGNLSDAFGFYESFPHRIVQFAEVEEKCTLVFSQQEFVTAWSTQVNPRTTLEADGCPYLYAIIHDSTTGTISGDFNLGVKLVGIKDFCGIGSNPGIDGSRLL  828
               SCOP domains d1ny721 2:1-182 Comovirus coat proteins (VP37 and VP23)                                                                                                                               d1ny722 2:183-369 Comovirus coat proteins (VP37 and VP23)                                                                                                                                   SCOP domains
               CATH domains 1ny7200 2:1-369  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains Como_LCP-1ny7201 2:1-369                                                                                                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author ...hhhhhhhhh...........eeeeeeeee........eeeeee.hhhhh.....hhhhhhhh.....eeeeeee.........eeeeeee.ee......hhhhhh..eeeee......eeeeee.........hhhhhhhh..eeeeeeee.........eeeeeeeeee........ee...eeeeeeeeeeeeeeee.......eeeee......eee..eee.hhhhhhhh.eeeeeeeeeeeeee.........eeeeeee........hhhhh.eeee.......eeeeeehhhhh...ee.......hhhhh..eeeeeee...........eeeeeeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ny7 2    1 MEQNLFALSLDDTSSVRGSLLDTKFAQTRVLLSKAMAGGDVLLDEYLYDVVNGQDFRATVAFLRTHVITGKIKVTATTNISDNSGCCLMLAINSGVRGKYSTDVYTICSQDSMTWNPGCKKNFSFTFNPNPCGDSWSAEMISRSRVRMTVICVSGWTLSPTTDVIAKLDWSIVNEKCEPTIYHLADCQNWLPLNRWMGKLTFPQGVTSEVRRMPLSIGGGAGATQAFLANMPNSWISMWRYFRGELHFEVTKMSSPYIKATVTFLIAFGNLSDAFGFYESFPHRIVQFAEVEEKCTLVFSQQEFVTAWSTQVNPRTTLEADGCPYLYAIIHDSTTGTISGDFNLGVKLVGIKDFCGIGSNPGIDGSRLL  369
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
   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, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Como_SCP] (3)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain 1,2   (POL2_CPMVS | P03599)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0046740    transport of virus in host, cell to cell    The transport of a virus between adjacent cells in a multicellular organism.
cellular component
    GO:0044156    host cell junction    A plasma membrane part that forms a specialized region of connection between two host cells or between a host cell and the host extracellular matrix. At a host cell junction, anchoring proteins extend through the host plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0044219    host cell plasmodesma    A fine cytoplasmic channel, found in all higher plants, that connects the cytoplasm of one host cell to that of an adjacent host cell.
    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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    Ala 1:22 - Pro 1:23   [ RasMol ]  
 
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  1ny7
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL2_CPMVS | P03599: 2bfu 5a32 5a33 5fmo

(-) Related Entries Specified in the PDB File

1bmv A VIRUS IN THE SAME FAMILY