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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARTIFICIAL TOP COMPONENT OF TURNIP YELLOW MOSAIC VIRUS
 
Authors :  A. M. M. Van Roon, H. H. J. Bink, J. R. Plaisier, C. W. A. Pleij, J. P. Abrahams, N. S. Pannu
Date :  14 Jul 04  (Deposition) - 16 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.75
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Artificial Top Component, Capsid Protein, Tymv, Virus, Crystallography, Virus/Viral Protein, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. M. Van Roon, H. H. J. Bink, J. R. Plaisier, C. W. A. Pleij, J. P. Abrahams, N. S. Pannu
Crystal Structure Of An Empty Capsid Of Turnip Yellow Mosaic Virus.
J. Mol. Biol. V. 341 1205 2004
PubMed-ID: 15321716  |  Reference-DOI: 10.1016/J.JMB.2004.06.085
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TURNIP YELLOW MOSAIC VIRUS EMPTY CAPSID
    Chains: A, B, C
    Organism Scientific: TURNIP YELLOW MOSAIC VIRUS
    Organism Taxid: 12154
    Other Details: COAT PROTEIN WAS REPORTED TO BE ACETYLATED AT THE N-TERMINUS OF CHAINS A, B, AND C, BUT NO N-TERMINAL ACETYL GROUP WAS OBSERVED

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1W39)

(-) Sites  (0, 0)

(no "Site" information available for 1W39)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W39)

(-) Exons   (0, 0)

(no "Exon" information available for 1W39)

(-) 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:169
 aligned with COAT_TYMV | P03608 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:180
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
            COAT_TYMV    10 QDRTVTVATVLPAVPGPSPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPANSPVTPAQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d1w39a           _ A: Tymovirus coat protein                                                                                                                                         SCOP domains
               CATH domains 1w39A0           0 A:10-189  [code=2.60.120.20, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......-----------...eeeeeeeeeeeee....eeeeehhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhh..eeeeeeee.....hhhhh.......ee...........eeee........eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w39 A  10 QDRTVT-----------SPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPAQSPVTPAQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                 |   -       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
                                15          27                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with COAT_TYMV | P03608 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            COAT_TYMV     1 MEIDKELAPQDRTVTVATVLPAVPGPSPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPANSPVTPAQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d1w39b_ B: Tymovirus coat protein                                                                                                                                                             SCOP domains
               CATH domains 1w39B00 B:1-189  [code=2.60.120.20, no name defined]                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.......................eeeeeeeeeeee....eeeeehhhhhhhhhhhh..eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhh....eeeee.........eeee...................eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w39 B   1 MEIDKELAPQDRTVTVATVLPAVPGPSPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPAQSPVTPAQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                    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:189
 aligned with COAT_TYMV | P03608 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            COAT_TYMV     1 MEIDKELAPQDRTVTVATVLPAVPGPSPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPANSPVTPAQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d1w39c_ C: Tymovirus coat protein                                                                                                                                                             SCOP domains
               CATH domains 1w39C00 C:1-189  [code=2.60.120.20, no name defined]                                                                                                                                          CATH domains
           Pfam domains (1) ------Tymo_coat-1w39C01 C:7-178                                                                                                                                                   ----------- Pfam domains (1)
           Pfam domains (2) ------Tymo_coat-1w39C02 C:7-178                                                                                                                                                   ----------- Pfam domains (2)
           Pfam domains (3) ------Tymo_coat-1w39C03 C:7-178                                                                                                                                                   ----------- Pfam domains (3)
         Sec.struct. author .....ee.......................eeeeeeeeee......eeeeehhhhhhhhhhhh..eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhh....eeeee.........eeee........eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w39 C   1 MEIDKELAPQDRTVTVATVLPAVPGPSPLTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPTFPTTVGVCWVPAQSPVTPAQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (1, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COAT_TYMV | P03608)
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:0039617    T=3 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        COAT_TYMV | P03608: 1auy

(-) Related Entries Specified in the PDB File

1auy TURNIP YELLOW MOSAIC VIRUS