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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF EBOLA VIRUS VP30
 
Authors :  T. M. Muziol, B. Hartlieb, S. Becker, W. Weissenhorn
Date :  01 Sep 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vp30 Ebola Virus Protein, Transcription, Rna Binding, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Hartlieb, T. Muziol, W. Weissenhorn, S. Becker
Crystal Structure Of The C-Terminal Domain Of Ebola Virus Vp30 Reveals A Role In Transcription And Nucleocapsid Association.
Proc. Natl. Acad. Sci. Usa V. 104 624 2007
PubMed-ID: 17202263  |  Reference-DOI: 10.1073/PNAS.0606730104

(-) Compounds

Molecule 1 - MINOR NUCLEOPROTEIN VP30
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTB
    Expression System Strain: BL21 CODON +
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 142-272
    Gene: VP30
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 186538
    Synonym: TRANSCRIPTION ACTIVATOR VP30

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2I8B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I8B)

(-) Exons   (0, 0)

(no "Exon" information available for 2I8B)

(-) Sequences/Alignments

Asymmetric/Biological 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:127
 aligned with VP30_EBOZ5 | Q77DJ5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:128
                                   148       158       168       178       188       198       208       218       228       238       248       258        
           VP30_EBOZ5   139 GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-.eehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8b A 140 G-AITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVmTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLImFITAFLNIALQLPCESSAVVVSGLRTLVP 266
                            | |    148       158       168       178       188       198       208       218       228       238       248       258        
                            | |                                 177-MSE                                                     237-MSE                         
                          140 |                                                                                                                             
                            141                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:127
 aligned with VP30_EBOZM | Q05323 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:128
                                   148       158       168       178       188       198       208       218       228       238       248       258        
           VP30_EBOZM   139 GPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP 266
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-.eehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8b A 140 G-AITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVmTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLImFITAFLNIALQLPCESSAVVVSGLRTLVP 266
                            | |    148       158       168       178       188       198       208       218       228       238       248       258        
                          140 |                                 177-MSE                                                     237-MSE                         
                            141                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with VP30_EBOZ5 | Q77DJ5 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:142
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264  
           VP30_EBOZ5   125 RLANPTADDFQQEEGPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP 266
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------...----.eehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8b B 135 NLY------FQG----AITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVmTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLImFITAFLNIALQLPCESSAVVVSGLRTLVP 266
                              |    138 |    |144       154       164       174  |    184       194       204       214       224       234  |    244       254       264  
                            137    138 |  141                                 177-MSE                                                     237-MSE                         
                                     140                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with VP30_EBOZM | Q05323 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:142
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264  
           VP30_EBOZM   125 RLANPTADDFQQEEGPKITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFITAFLNIALQLPCESSAVVVSGLRTLVP 266
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------...----.eehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i8b B 135 NLY------FQG----AITLLTLIKTAEHWARQDIRTIEDSKLRALLTLCAVmTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLImFITAFLNIALQLPCESSAVVVSGLRTLVP 266
                              |    138 |    |144       154       164       174  |    184       194       204       214       224       234  |    244       254       264  
                            137    138 |  141                                 177-MSE                                                     237-MSE                         
                                     140
   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 2I8B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I8B)

(-) Gene Ontology  (8, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VP30_EBOZM | Q05323)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0044414    suppression of host defenses    Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host defense(s) by active mechanisms that normally result in the shutting down of a host pathway. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain A,B   (VP30_EBOZ5 | Q77DJ5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2i8b)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2i8b)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  2i8b
    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
  VP30_EBOZ5 | Q77DJ5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  VP30_EBOZM | Q05323
    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
  VP30_EBOZ5 | Q77DJ5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VP30_EBOZM | Q05323
    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
        VP30_EBOZ5 | Q77DJ5: 5vao 5vap
        VP30_EBOZM | Q05323: 5dvw 5t3t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2I8B)