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(-) Description

Title :  PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION
 
Authors :  Z. Chen, C. Stauffacher, Y. Li, T. Schmidt, W. Bomu, G. Kamer, M. Shanks, G. Lomonossoff, J. E. Johnson
Date :  09 Oct 89  (Deposition) - 09 Oct 89  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  M,1,2
Biol. Unit 1:  M,1,2  (60x)
Keywords :  Protein-Rna Complex, Single Strand, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. G. Chen, C. Stauffacher, Y. Li, T. Schmidt, W. Bomu, G. Kamer, M. Shanks, G. Lomonossoff, J. E. Johnson
Protein-Rna Interactions In An Icosahedral Virus At 3. 0 A Resolution.
Science V. 245 154 1989
PubMed-ID: 2749253
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)
    Chains: 1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Organism Scientific: BEAN POD MOTTLE VIRUS
    Organism Taxid: 12260
 
Molecule 2 - PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)
    Chains: 2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Organism Scientific: BEAN POD MOTTLE VIRUS
    Organism Taxid: 12260
 
Molecule 3 - RNA (5'-R(*GP*GP*UP*CP*AP*AP*AP*AP*UP*GP*C)-3')
    Chains: M
    Engineered: YES
    Other Details: M
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : M12
Biological Unit 1 (60x): M12

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BMV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn 2:2007 -Pro 2:2008

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BMV)

(-) 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 d1bmv11 1:1001-1185 Comovirus coat proteins (VP37 and VP23)                                                                                                                               SCOP domains
               CATH domains 1bmv100 1:1001-1185  [code=2.60.120.20, no name defined]                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...........eeeeeee...eeeee.....eee...hhhhhhhhhh.eeeeeeeeeeeeeee..........eeeeeee.........eeeeee...eeeeeeeeeee...................eeeeeeee...eeeeeeeeeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1bmv 1 1001 SISQQTVWNQMATVRTPLNFDSSKQSFCQFSVDLLGGGISVDKTGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNAAVKRSDWASLVQVFLTNSNSTEHFDACRWTKSEPHSWELIFPIEVCGPNNGFEMWSSEWANQTSWHLSFLVDNPKQSTTFDVLLGISQNFEIAGNTLMPAFSVPQ 1185
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180     


Chain 2 from PDB  Type:PROTEIN  Length:374
 aligned with POL2_BPMV | P23009 from UniProtKB/Swiss-Prot  Length:1018

    Alignment length:374
                                   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 METNLFKLSLDDVETPKGSMLDLKISQSKIALPKNTVGGTILRSDLLANFLTEGNFRASVDLQRTHRIKGMIKMVATVGIPENTGIALACAMNSSIRGRASSDIYTICSQDCELWNPACTKAMTMSFNPNPCSDAWSLEFLKRTGFHCDIICVTGWTATPMQDVQVTIDWFISSQECVPRTYCVLNPQNPFVLNRWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNAVLSMWRYFVGDLVFEVSKMTSPYIKCTVSFFIAFGNLADDTINFEAFPHKLVQFGEIQEKVVLKFSQEEFLTAWSTQVRPATTLLADGCPYLYAMVHDSSVSTIPGDFVIGVKLTIIENMCAYGLNPGISGSRLLGTIPQ  820
               SCOP domains d1bmv21 2:3001-3182 Comovirus coat proteins (VP37 and VP23)                                                                                                                           d1bmv22 2:2001-2189 Comovirus coat proteins (VP37 and VP23)                                                                                                                                  --- SCOP domains
               CATH domains 1bmv200 2:3001-2192  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ......................eeeeeeeeee......eeeeeeehhhhhh......hhhhhhh.......eeeeeee........eeeeeee..........hhhhh..eeeee.....eeeeeee................hhhhhhhhhhhhhh......eeeeeeeee....................eeeeeeeeee..eeeeeeeee.......eee..eee..hhhhhhhhh..eeeeeeeeeeee.....eeeeeeeee................eee......eeeeeee..........................eeeeeeeee.......eeeeeeeeeeeeee................... Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------eeeeeee----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1bmv 2 3001 METNLFKLSLDDVETPKGSMLDLKISQSKIALPKNTVGGTILRSDLLANFLTEGNFRASVDLQRTHRIKGMIKMVATVGIPENTGIALACAMNSSIRGRASSDIYTICSQDCELWNPACTKAMTMSFNPNPCSDAWSLEFLKRTGFHCDIICVTGWTATPMQDVQVTIDWFISSQECVPRTYCVLNPQNPFVLNRWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNAVLSMWRYFVGDLVFEVSKMTSPYIKCTVSFFIAFGNLADDTINFEAFPHKLVQFGEIQEKVVLKFSQEEFLTAWSTQVRPATTLLADGCPYLYAMVHDSSVSTIPGDFVIGVKLTIIENMCAYGLNPGISGSRLLGTIPQ 2192
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180 ||   2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188    
                                                                                                                                                                                                              3182|                                                                                                                                                                                               
                                                                                                                                                                                                               2001                                                                                                                                                                                               


Chain M from PDB  Type:RNA  Length:11
                                            
                1bmv M    1 GGUCAAAAUGC   11
                                    10
   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  (0, 0)

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

(-) 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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  1bmv
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 Related Entries

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        POL2_BPMV | P23009: 1pgl 1pgw

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