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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORNA DISEASE VIRUS MATRIX PROTEIN (BDV-M) REVEALS RNA BINDING PROPERTIES
 
Authors :  P. Neumann, D. Lieber, S. Meyer, P. Dautel, A. Kerth, I. Kraus, W. Garten, M. T. Stubbs
Date :  28 Oct 08  (Deposition) - 03 Feb 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Viral Matrix Protein, Rna Binding, Membrane Binding, Viruses, Ssrna Negative-Strand Viruses, Mononegavirales; Bornaviridae, Bornavirus, Alternative Splicing, Cytoplasm, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Neumann, D. Lieber, S. Meyer, P. Dautel, A. Kerth, I. Kraus, W. Garten, M. T. Stubbs
Crystal Structure Of The Borna Disease Virus Matrix Protein (Bdv-M) Reveals Ssrna Binding Properties
Proc. Natl. Acad. Sci. Usa V. 106 3710 2009
PubMed-ID: 19237566  |  Reference-DOI: 10.1073/PNAS.0808101106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATRIX PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMAL-C2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: M
    Organism Common: BDV
    Organism Scientific: BORNA DISEASE VIRUS
    Organism Taxid: 12455
    Synonym: GP18, P16

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1C5P4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:36 , PHE A:37 , LYS A:111 , HIS A:112 , ASN A:115 , HOH A:226BINDING SITE FOR RESIDUE C5P A 300
2AC2SOFTWAREARG A:126 , ASN A:127BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWARETYR A:93 , HOH A:219BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWARELYS A:55BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F1J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MATRX_BDV1_001 *E108DMATRX_BDV1  ---  ---AE108D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MATRX_BDV1_001 *E108DMATRX_BDV1  ---  ---AE108D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F1J)

(-) Exons   (0, 0)

(no "Exon" information available for 3F1J)

(-) 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:140
 aligned with MATRX_BDV1 | P0C794 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
           MATRX_BDV1     3 SKHSYVELKDKVIVPGWPTLMLEIDFVGGTSRNQFLNIPFLSVKEPLQLPREKKLTDYFTIDVEPAGHSLVNIYFQIDDFLLLTLNSLSVYKDPIRKYMFLRLNKEQSKHAINAAFNVFSYRLRNIGVGPLGPDIRSSGP 142
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhh.....eeeeeee.........eeeeeeee...........hhhhheeeeeee.....eeeeeeehhhhhhhhhhhh........eeeee.hhhhhhhhhhh.....eeeeeee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------D---------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1j A   3 SKHSYVELKDKVIVPGWPTLmLEIDFVGGTSRNQFLNIPFLSVKEPLQLPREKKLTDYFTIDVEPAGHSLVNIYFQIDDFLLLTLNSLSVYKDPIRKYmFLRLNKEQSKHAINAAFNVFSYRLRNIGVGPLGPDIRSSGP 142
                                    12        22|       32        42        52        62        72        82        92       102       112       122       132       142
                                               23-MSE                                                                       101-MSE                                     


Chain A from PDB  Type:PROTEIN  Length:140
 aligned with MATRX_BDVV | P0C795 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
           MATRX_BDVV     3 SKHSYVELKDKVIVPGWPTLMLEIDFVGGTSRNQFLNIPFLSVKEPLQLPREKKLTDYFTIDVEPAGHSLVNIYFQIDDFLLLTLNSLSVYKDPIRKYMFLRLNKDQSKHAINAAFNVFSYRLRNIGVGPLGPDIRSSGP 142
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhh.....eeeeeee.........eeeeeeee...........hhhhheeeeeee.....eeeeeeehhhhhhhhhhhh........eeeee.hhhhhhhhhhh.....eeeeeee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------D---------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1j A   3 SKHSYVELKDKVIVPGWPTLmLEIDFVGGTSRNQFLNIPFLSVKEPLQLPREKKLTDYFTIDVEPAGHSLVNIYFQIDDFLLLTLNSLSVYKDPIRKYmFLRLNKEQSKHAINAAFNVFSYRLRNIGVGPLGPDIRSSGP 142
                                    12        22|       32        42        52        62        72        82        92       102       112       122       132       142
                                               23-MSE                                                                       101-MSE
   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 3F1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F1J)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (MATRX_BDV1 | P0C794)
molecular function
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain A   (MATRX_BDVV | P0C795)
molecular function
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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
    C5P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3f1j)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3f1j
    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
  MATRX_BDV1 | P0C794
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MATRX_BDVV | P0C795
    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
  MATRX_BDV1 | P0C794
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MATRX_BDVV | P0C795
    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
        MATRX_BDV1 | P0C794: 4hi5 4hi6 4hit 4hiu 4hiw 4hiy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3F1J)