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(-) Description

Title :  DESMODIUM YELLOW MOTTLE TYMOVIRUS
 
Authors :  S. B. Larson, J. Day, M. A. Canady, A. Greenwood, A. Mcpherson
Date :  10 Nov 99  (Deposition) - 30 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (60x)
Keywords :  Plant Virus, Dymv, Capsid Protein, Coat Protein, Tymoviruses, Water Structure, Rna, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Larson, J. Day, M. A. Canady, A. Greenwood, A. Mcpherson
Refined Structure Of Desmodium Yellow Mottle Tymovirus At 2. 7 A Resolution.
J. Mol. Biol. V. 301 625 2000
PubMed-ID: 10966774  |  Reference-DOI: 10.1006/JMBI.2000.3983
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
    Chains: D
    Engineered: YES
    Fragment: VIRAL RNA FRAGMENT
    Synthetic: YES
 
Molecule 2 - RNA (5'-R(P*UP*U)-3')
    Chains: E
    Engineered: YES
    Fragment: VIRAL RNA FRAGMENT
    Synthetic: YES
 
Molecule 3 - DESMODIUM YELLOW MOTTLE VIRUS
    Chains: A, B, C
    Fragment: VIRAL COAT PROTEIN
    Organism Scientific: DESMODIUM YELLOW MOTTLE VIRUS
    Organism Taxid: 70821

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (60x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1DDL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DDL)

(-) 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:188
 aligned with O89511_9VIRU | O89511 from UniProtKB/TrEMBL  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         O89511_9VIRU     1 MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
               SCOP domains d1ddla_ A: Tymovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1ddlA00 A:1-188  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......................eeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhhh...eeeee.........eeee........eee........eeeeeeee..........eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddl A   1 MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with O89511_9VIRU | O89511 from UniProtKB/TrEMBL  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         O89511_9VIRU     1 MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
               SCOP domains d1ddlb_ B: Tymovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1ddlB00 B:1-188  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......................eeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhh....eeeee.........eeee........eee........eeeeeeee..........eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddl B   1 MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain C from PDB  Type:PROTEIN  Length:175
 aligned with O89511_9VIRU | O89511 from UniProtKB/TrEMBL  Length:188

    Alignment length:175
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
         O89511_9VIRU    14 NTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
               SCOP domains d1ddlc_ C: Tymovirus coat protein                                                                                                                                               SCOP domains
               CATH domains 1ddlC00 C:14-188  [code=2.60.120.20, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhhh...eeeee.........eeee........eee........eeeeeeee..........eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddl C  14 NTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS 188
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     


Chain D from PDB  Type:RNA  Length:7
                                       
                 1ddl D   1 UUUUUUU   7


Chain E from PDB  Type:RNA  Length:2
                                  
                 1ddl E   1 UU   2
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (O89511_9VIRU | O89511)
molecular function
    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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