Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF TURNIP YELLOW MOSAIC VIRUS 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,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Plant Virus, Coat Protein, Capsid Protein, Tymoviruses, Tymv, Rna, Icosahedral Virus, Virus-Rna Complex (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
    Fragment: VIRAL COAT PROTEIN
    Organism Scientific: TURNIP YELLOW MOSAIC VIRUS
    Organism Taxid: 12155
    Strain: (AUSTRALIAN ISOLATE)
    Synonym: VIRION PROTEIN
 
Molecule 2 - 5'-R(*CP*CP*C)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (60x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FZ2)

(-) Sites  (0, 0)

(no "Site" information available for 2FZ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 2FZ2)

(-) 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:164
 aligned with COAT_TYMVA | P20125 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:164
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
           COAT_TYMVA    26 PSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPANSPVTPTQITKTYGGQIFCIGGAINTLSPLIVKCPLEMMNPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
               SCOP domains d2fz2a_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains 2fz2A00 A:26-189  [code=2.60.120.20, no name defined]                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeee...hhhhhhhh..eeeeeeeeeeeeeee.hhhhhh.eeeeeeeee.....hhhhhhhh...eeeee..........eee.hhhhh..eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz2 A  26 PSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPAQSPVTPTQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    


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 d2fz2b_ B: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2fz2B00 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
                 2fz2 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 d2fz2c_ C: automated matches                                                                                                                                                                  SCOP domains
               CATH domains 2fz2C00 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.....hhhhhhhh...eeeee.........eeee.hhhhh..eee........eeeeeeee..........eeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz2 C   1 MEIDKELAPQDRTVTVATVLPTVPGPSPFTIKQPFQSEVLFAGTKDAEASLTIANIDSVSTLTTFYRHASLESLWVTIHPTLQAPAFPTTVGVCWVPAQSPVTPTQITKTYGGQIFCIGGAIQTLSPLIVKCPLEMMQPRVKDSIQYLDSPKLLISITAQPTAPPASTCIITVSGTLSMHSPLITDTST 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain D from PDB  Type:RNA  Length:3
                                   
                 2fz2 D   1 CCC   3
   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 2FZ2)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2fz2)
 
  Sites
(no "Sites" information available for 2fz2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fz2)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2fz2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  COAT_TYMVA | P20125
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  COAT_TYMVA | P20125
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        COAT_TYMVA | P20125: 2fz1

(-) Related Entries Specified in the PDB File

1auy THE SAME STRUCTURE DONE AT ROOM TEMPERATURE.
1w39 THE STRUCTURE AT 100 K IN A DIFFERENT SPACE GROUP OF THE SAME VIRUS WITH THE RNA REMOVED PRIOR TO CRYSTALLIZATION.
2fz1 THE STRUCTURE AT 100 K OF THE SAME VIRUS WITH THE RNA REMOVED PRIOR TO CRYSTALLIZATION.