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

(-) Description

Title :  STRUCTURE OF THE LAGOS BAT VIRUS MATRIX PROTEIN
 
Authors :  S. C. Graham, R. Assenberg, O. Delmas, A. Verma, A. Gholami, C. Talbi, R. J. Owens, D. I. Stuart, J. M. Grimes, H. Bourhy
Date :  03 Nov 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral Assembly, Viral Morphogenesis, Lagos Bat Virus, Polymer, Viral Protein, Matrix Protein, Vsv (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Graham, R. Assenberg, O. Delmas, A. Verma, A. Gholami, C. Talbi, R. J. Owens, D. I. Stuart, J. M. Grimes, H. Bourhy
Rhabdovirus Matrix Protein Structures Reveal A Novel Mode Of Self-Association.
Plos Pathog. V. 4 251 2008
PubMed-ID: 19112510  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1000251
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATRIX PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINS
    Expression System Strain: ROSETTA PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LAGOS BAT VIRUS
    Organism Taxid: 38766
    Other Details: ISOLATE 8619NGA, GENOTYPE 2, ISOLATED FROM A FRUGIVOROUS BAT IN NIGERIA (BOULGER, L. R., AND J. S. PORTEFIELD. 1958. ISOLATION OF A VIRUS FROM NIGERIAN FRUIT BATS. TRANS.R.SOC.TROP.MED.HYG. 52:421-424.)
    Synonym: LAGOS BAT VIRUS MATRIX PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2W2S)

(-) Sites  (0, 0)

(no "Site" information available for 2W2S)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:162

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W2S)

(-) Exons   (0, 0)

(no "Exon" information available for 2W2S)

(-) 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:163
 aligned with MATRX_LBV | Q6JAM6 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:173
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
            MATRX_LBV    30 DLWMPPPEYVPLTQIKGKENVRNFCINGEIKICSPNGYSFRILRHILKSFDNVYSGNRRLIGVVKVVIGLVLSASPVPEGMNWVYKLRRTLIFQWAESHGPLEGEELEYSQEITWDDEAEFVSLQIRVSAKQCHIQGRLWCINMNSKACQLWADMGLKTQQSQEDENTSLLLE 202
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Rhabdo_M          2-2w2sA01 A:30-202                                                                                                                                          Pfam domains
         Sec.struct. author ..ee....----------.eeeeeeeeeeeeee....eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eee..eeeeeeeeeeeeee...........eeeeeeeeeee..eeeeeeeeeeeee.....ee.....hhhhhhhhhhh...eee.......eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2s A  30 DLWMPPPE----------ENVRNFCINGEIKICSPNGYSFRILRHILKSFDNVYSGNRRLIGVVKVVIGLVLSASPVPEGMNWVYKLRRTLIFQWAESHGPLEGEELEYSQEITWDDEAEFVSLQIRVSAKQCHIQGRLWCINMNSKACQLWADMGLKTQQSQEDENTSLLLE 202
                                   | -        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
                                  37         48
   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 2W2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W2S)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Rhabdo_M2] (1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MATRX_LBV | Q6JAM6)
molecular function
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
biological process
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0033645    host cell endomembrane system    A collection of membranous structures involved in transport within the host cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

 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
(no "Ligands, Modified Residues, Ions" information available for 2w2s)
 
  Sites
(no "Sites" information available for 2w2s)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w2s)
 

(-) 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
  2w2s
    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_LBV | Q6JAM6
    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_LBV | Q6JAM6
    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 2W2S)

(-) Related Entries Specified in the PDB File

2w2r STRUCTURE OF THE VESICULAR STOMATITIS VIRUS MATRIX PROTEIN