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 :  CRYSTAL STRUCTURE OF RNA SILENCING SUPPRESSOR P21 FROM BEET YELLOWS VIRUS
 
Authors :  K. Ye, D. J. Patel
Date :  22 Jun 05  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Octamer, Ring, Head-To-Head, Tail-To-Tail, All Alpha Helical, Rna- Binding Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ye, D. J. Patel
Rna Silencing Suppressor P21 Of Beet Yellows Virus Forms An Rna Binding Octameric Ring Structure
Structure V. 13 1375 2005
PubMed-ID: 16154094  |  Reference-DOI: 10.1016/J.STR.2005.06.017

(-) Compounds

Molecule 1 - RNA SILENCING SUPPRESSOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: P21
    Organism Scientific: BEET YELLOWS VIRUS
    Organism Taxid: 12161
    Synonym: P21

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2CWO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CWO)

(-) 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:165
 aligned with P21_BYVU | Q08545 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
             P21_BYVU     1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwo A   1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQ------------RIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
                                    10        20        30        40        50        60   |     -      | 80        90       100       110       120       130       140       150       160       170       
                                                                                          64           77                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with P21_BYVU | Q08545 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
             P21_BYVU     1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwo B   1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQ------------RIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
                                    10        20        30        40        50        60   |     -      | 80        90       100       110       120       130       140       150       160       170       
                                                                                          64           77                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:165
 aligned with P21_BYVU | Q08545 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
             P21_BYVU     1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------------hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwo C   1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQ------------RIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
                                    10        20        30        40        50        60   |     -      | 80        90       100       110       120       130       140       150       160       170       
                                                                                          64           77                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:165
 aligned with P21_BYVU | Q08545 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
             P21_BYVU     1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQHPNQSSKLRVPSRIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwo D   1 MKFFLKDGETSRALSRSESLLRRVKELGTNSQQSEISECVDEFNELASFNHLLVTVEHREWMEQ------------RIGEMLKEIRAFLKVRVVTPMHKETASDTLNAFLEEYCRITGLAREDALREKMRKVKSVVLFHHSELLKFEVTENMFSYTELLKLNLSLRVISSQILGMAI 177
                                    10        20        30        40        50        60   |     -      | 80        90       100       110       120       130       140       150       160       170       
                                                                                          64           77
   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  (0, 0)

(no "SCOP Domain" information available for 2CWO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CWO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (P21_BYVU | Q08545)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

 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 2cwo)
 
  Sites
(no "Sites" information available for 2cwo)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cwo)
 
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
  2cwo
    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
  P21_BYVU | Q08545
    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
  P21_BYVU | Q08545
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2CWO)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CWO)