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(-) Description

Title :  RICE YELLOW MOTTLE VIRUS
 
Authors :  C. Qu, L. Liljas, N. Opalka, C. Brugidou, M. Yeager, R. N. Beachy, C. M. Fauquet, J. E. Johnson, T. Lin
Date :  26 May 00  (Deposition) - 01 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Plant Virus, Capsid Protein, Coat Protein, Beta-Annulus, Domain Swapping, X-Ray Diffraction, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Qu, L. Liljas, N. Opalka, C. Brugidou, M. Yeager, R. N. Beachy, C. M. Fauquet, J. E. Johnson, T. Lin
3D Domain Swapping Modulates The Stability Of Members Of An Icosahedral Virus Group.
Structure Fold. Des. V. 8 1095 2000
PubMed-ID: 11080631  |  Reference-DOI: 10.1016/S0969-2126(00)00508-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C
    Organism Scientific: RICE YELLOW MOTTLE VIRUS
    Organism Taxid: 31744
    Other Details: COLLECTED FROM RICE FIELD IN THE IVORY COAST AND WAS PROPAGATED UNDER CONTAINED CONDITIONS IN A SUSCEPTIBLE RICE VARIETY IR8 (ORYZA SATIVA L.)

 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
1AC1SOFTWAREVAL A:182 , ASN A:237 , THR A:238 , ASP C:126 , ASP C:129BINDING SITE FOR RESIDUE CA C 1001
2AC2SOFTWAREASP A:126 , ASP A:129 , VAL B:182 , ASN B:237 , THR B:238BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWAREASP B:126 , ASP B:129 , VAL C:182 , ASN C:237 , THR C:238BINDING SITE FOR RESIDUE CA B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F2N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F2N)

(-) Exons   (0, 0)

(no "Exon" information available for 1F2N)

(-) 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 Q86527_9VIRU | Q86527 from UniProtKB/TrEMBL  Length:239

    Alignment length:189
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
         Q86527_9VIRU    51 LSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 239
               SCOP domains d1f2na_ A: Sobemovirus coat protein                                                                                                                                                           SCOP domains
               CATH domains 1f2nA00 A:50-238  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee.......eeee.hhhhhhhhhhhhh...eeee...eeeeee........eeeeeee.........hhhhhhh....eeee...hhhhhhhh.........eee........ee.........hhhhhh.....eeeeee.......eeeeeeeeeeeeee....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2n A  50 LSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 238
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229         


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with Q86527_9VIRU | Q86527 from UniProtKB/TrEMBL  Length:239

    Alignment length:189
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
         Q86527_9VIRU    51 LSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 239
               SCOP domains d1f2nb_ B: Sobemovirus coat protein                                                                                                                                                           SCOP domains
               CATH domains 1f2nB00 B:50-238  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeeee.......eeee.hhhhhhhhhhhhh...eeee...eeeeee........eeeeeee.........hhhhhhhh...eeee...hhhhhhhhh........eee........ee.........hhhhhhh....eeeeee.......eeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2n B  50 LSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 238
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229         


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q86527_9VIRU | Q86527 from UniProtKB/TrEMBL  Length:239

    Alignment length:212
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  
         Q86527_9VIRU    28 AEPQLQRAPVAQASRISGTVPGPLSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 239
               SCOP domains d1f2nc_ C: Sobemovirus coat protein                                                                                                                                                                                  SCOP domains
               CATH domains 1f2nC00 C:27-238  [code=2.60.120.20, no name defined]                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..........eeeeeeeeeeeeeee.......eeee.hhhhhhhhhhhhh.eeeeee...eeeeee........eeeeeee.........hhhhhhh....eeee...hhhhhhh....hhhhheeee........ee.........hhhhhhh....eeeeee.......eeeeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2n C  27 AEPQLQRAPVAQASRISGTVPGPLSSNTWPLHSVEFLADFKRSSTSADATTYDCVPFNLPRVWSLARCYSMWKPTRWDVVYLPEVSATVAGSIEMCFLYDYADTIPRYTGKMSRTAGFVTSSVWYGAEGCHLLSGGSARNAVVASMDCSRVGWKRVTSSIPSSVDPNVVNTILPARLAVRSSIKPTVSDTPGKLYVIASMVLRDPVDPTLNT 238
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
   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 1F2N)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q86527_9VIRU | Q86527)
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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