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(-) Description

Title :  STRUCTURE OF EMPTY HEAD TURNIP YELLOW MOSAIC VIRUS (ATC) AT 100 K
 
Authors :  S. B. Larson, R. W. Lucas, A. Mcpherson
Date :  08 Feb 06  (Deposition) - 21 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Plant Virus, Coat Protein, Capsid Protein, Tymoviruses, Tymv, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Larson, R. W. Lucas, A. Greenwood, A. Mcpherson
The Rna Of Turnip Yellow Mosaic Virus Exhibits Icosahedral Order.
Virology V. 334 245 2005
PubMed-ID: 15780874  |  Reference-DOI: 10.1016/J.VIROL.2005.01.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: BRASSICA RAPA SUBSP. CHINENSIS
    Expression System Strain: SUBSP. CHINENSIS
    Expression System Taxid: 93385
    Organism Scientific: TURNIP YELLOW MOSAIC VIRUS
    Organism Taxid: 12155
    Strain: (AUSTRALIAN ISOLATE)
    Synonym: VIRION PROTEIN

 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 2FZ1)

(-) Sites  (0, 0)

(no "Site" information available for 2FZ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FZ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FZ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 2FZ1)

(-) 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:163
 aligned with COAT_TYMVA | P20125 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:163
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   
           COAT_TYMVA    27 SPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPANSPVTPTQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d2fz1a_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2fz1A00 A:27-189  [code=2.60.120.20, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee.........eeeeeeee.....hhhhhhhh...eee............eee.hhhhh..eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz1 A  27 SPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPAQSPVTPTQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186   


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with COAT_TYMVA | P20125 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_TYMVA     1 MEIDKELAPQDRTVTVATVLPTVPGPSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPANSPVTPTQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d2fz1b_ B: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2fz1B00 B:1-189  [code=2.60.120.20, no name defined]                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee......................eeeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeeeee.....hhhhhhhh...eeeee.........eeee.hhhhh..eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz1 B   1 MEIDKELAPQDRTVTVATVLPTVPGPSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPAQSPVTPTQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 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_TYMVA | P20125 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_TYMVA     1 MEIDKELAPQDRTVTVATVLPTVPGPSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPANSPVTPTQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d2fz1c_ C: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2fz1C00 C:1-189  [code=2.60.120.20, no name defined]                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee......................eeeeeeeeeeeee....eeeeee...hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeeeee.....hhhhh......eeeee.........eeee.hhhhh.............eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz1 C   1 MEIDKELAPQDRTVTVATVLPTVPGPSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPAQSPVTPTQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 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  (0, 0)

(no "Pfam Domain" information available for 2FZ1)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COAT_TYMVA | P20125)
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_TYMVA | P20125: 2fz2

(-) Related Entries Specified in the PDB File

1auy THE STRUCTURE OF THE SAME VIRAL COAT PROTEIN CONTAINING RNA DONE AT ROOM TEMPERATURE.
1fz2 THE STRUCTURE OF THE SAME VIRAL COAT PROTEIN CONTAINING RNA DONE AT 100 K.
1w39 THE STRUCTURE AT 100 K IN A DIFFERENT SPACE GROUP OF THE SAME VIRUS WITH THE RNA REMOVED PRIOR TO CRYSTALLIZATION.