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(-) Description

Title :  BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT
 
Authors :  T. Lin, J. Cavarelli, J. E. Johnson
Date :  28 May 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  1,2,3
Biol. Unit 1:  1,2,3  (60x)
Keywords :  Comovirus, Virus, Viral Coat Protein, Bean Pod Mottle Virus (Bpmv), Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lin, J. Cavarelli, J. E. Johnson
Evidence For Assembly-Dependent Folding Of Protein And Rna In An Icosahedral Virus.
Virology V. 314 26 2003
PubMed-ID: 14517057  |  Reference-DOI: 10.1016/S0042-6822(03)00457-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
    Chains: 1
    Organism Scientific: BEAN-POD MOTTLE VIRUS (STRAIN KENTUCKY G7)
    Organism Taxid: 31715
    Strain: KENTUCKY G7
    Synonym: BPMV, GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37
 
Molecule 2 - BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
    Chains: 2
    Organism Scientific: BEAN-POD MOTTLE VIRUS (STRAIN KENTUCKY G7)
    Organism Taxid: 31715
    Strain: KENTUCKY G7
    Synonym: BPMV, GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37
 
Molecule 3 - 5'-R(*AP*GP*UP*CP*UP*C)-3'
    Chains: 3
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1PGL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn 2:189 -Pro 2:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PGL)

(-) 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:185
 aligned with POL2_BPMV | P23009 from UniProtKB/Swiss-Prot  Length:1018

    Alignment length:185
                                   830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000     
           POL2_BPMV    821 SISQQTVWNQMATVRTPLNFDSSKQSFCQFSVDLLGGGISVDKTGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNAAVKRSDWASLVQVFLTNSNSTEHFDACRWTKSEPHSWELIFPIEVCGPNNGFEMWSSEWANQTSWHLSFLVDNPKQSTTFDVLLGISQNFEIAGNTLMPAFSVPQ 1005
               SCOP domains d1pgl11 1:1-185 Comovirus coat proteins (VP37 and VP23)                                                                                                                                   SCOP domains
               CATH domains 1pgl100 1:1-185  [code=2.60.120.20, no name defined]                                                                                                                                      CATH domains
               Pfam domains Como_SCP-1pgl101 1:1-184                                                                                                                                                                - Pfam domains
         Sec.struct. author ........eeeeeee...........eeeeeee....eeee......eeee..hhhhhhhhheeeeeeeeeeeeeee.....hhhhh..eeeeeee..........eeeee....eeeeeeeeee....................eeeeeee......eeeeeeee....eeeeeee...ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pgl 1    1 SISQQTVWNQMATVRTPLNFDSSKQSFCQFSVDLLGGGISVDKTGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNAAVKRSDWASLVQVFLTNSNSTEHFDACRWTKSEPHSWELIFPIEVCGPNNGFEMWSSEWANQTSWHLSFLVDNPKQSTTFDVLLGISQNFEIAGNTLMPAFSVPQ  185
                                    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:370
 aligned with POL2_BPMV | P23009 from UniProtKB/Swiss-Prot  Length:1018

    Alignment length:370
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816
           POL2_BPMV    447 METNLFKLSLDDVETPKGSMLDLKISQSKIALPKNTVGGTILRSDLLANFLTEGNFRASVDLQRTHRIKGMIKMVATVGIPENTGIALACAMNSSIRGRASSDIYTICSQDCELWNPACTKAMTMSFNPNPCSDAWSLEFLKRTGFHCDIICVTGWTATPMQDVQVTIDWFISSQECVPRTYCVLNPQNPFVLNRWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNAVLSMWRYFVGDLVFEVSKMTSPYIKCTVSFFIAFGNLADDTINFEAFPHKLVQFGEIQEKVVLKFSQEEFLTAWSTQVRPATTLLADGCPYLYAMVHDSSVSTIPGDFVIGVKLTIIENMCAYGLNPGISGSRLLG  816
               SCOP domains d1pgl21 2:1-182 Comovirus coat proteins (VP37 and VP23)                                                                                                                               d1pgl22 2:183-370 Comovirus coat proteins (VP37 and VP23)                                                                                                                                    SCOP domains
               CATH domains 1pgl200 2:1-370  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains Como_LCP-1pgl201 2:1-370                                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author ...hhhhh...............eeeeeeeee........eeeeeehhhhh......hhhhhhhh....eeeeeeee.........eeeeeee.ee......hhhhhh..eeeee......eeeeee.........hhhhhhhhh.eeeeeeee.........eeeeeeeeeeeee.....ee.......eeeeeeeeeeee........eeee......eee..eee.hhhhhhhh.eeeeeeeeeeeeee.........eeeeee.........hhhhh.eeee.......eeeeeehhhhh...ee...............eeeeee...........eeeeeeeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pgl 2    1 METNLFKLSLDDVETPKGSMLDLKISQSKIALPKNTVGGTILRSDLLANFLTEGNFRASVDLQRTHRIKGMIKMVATVGIPENTGIALACAMNSSIRGRASSDIYTICSQDCELWNPACTKAMTMSFNPNPCSDAWSLEFLKRTGFHCDIICVTGWTATPMQDVQVTIDWFISSQECVPRTYCVLNPQNPFVLNRWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNAVLSMWRYFVGDLVFEVSKMTSPYIKCTVSFFIAFGNLADDTINFEAFPHKLVQFGEIQEKVVLKFSQEEFLTAWSTQVRPATTLLADGCPYLYAMVHDSSVSTIPGDFVIGVKLTIIENMCAYGLNPGISGSRLLG  370
                                    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       370


Chain 3 from PDB  Type:RNA  Length:6
                                       
                1pgl 3    1 AGUCUC    6
   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_BPMV | P23009)
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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    Asn 2:189 - Pro 2:190   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL2_BPMV | P23009: 1bmv 1pgw

(-) Related Entries Specified in the PDB File

1bmv UNREFINED STRUCTURE
1ny7 COWPEA MOSAIC VIRUS; A VIRUS IN THE SAME FAMILY
1pgw BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT