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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PARAMYXOVIRUS SV5 FUSION PROTEIN CORE
 
Authors :  K. A. Baker, R. E. Dutch, R. A. Lamb, T. S. Jardetzky
Date :  27 Feb 99  (Deposition) - 26 Mar 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Paramyxovirus, Fusion, Sv5, Coiled-Coil, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Baker, R. E. Dutch, R. A. Lamb, T. S. Jardetzky
Structural Basis For Paramyxovirus-Mediated Membrane Fusion
Mol. Cell V. 3 309 1999
PubMed-ID: 10198633  |  Reference-DOI: 10.1016/S1097-2765(00)80458-X

(-) Compounds

Molecule 1 - PROTEIN (FUSION GLYCOPROTEIN)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: N1
    Expression System Plasmid: PGEX-4T-1-N1, PGEX-4T-1-N1
    Expression System Strain: DH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: POST FUSION CORE (RESIDUE 122-185)
    Gene: FUSION PROTEIN
    Mutation: YES
    Organism Scientific: SIMIAN VIRUS 5 (STRAIN W3)
    Organism Taxid: 11208
    Other Details: 4 PUTATIVE CHLORIDE IONS INCLUDED
    Other Details - Source: CLEAVED GST FUSION
    Strain: W3
 
Molecule 2 - PROTEIN (FUSION GLYCOPROTEIN)
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: N1
    Expression System Plasmid: PGEX-4T-1-N1, PGEX-4T-1-N1
    Expression System Strain: DH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: POST FUSION CORE (RESIDUE 440-477)
    Gene: FUSION PROTEIN
    Organism Scientific: SIMIAN VIRUS 5 (STRAIN W3)
    Organism Taxid: 11208
    Other Details: 4 PUTATIVE CHLORIDE IONS INCLUDED
    Other Details - Source: CLEAVED GST FUSION
    Strain: W3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:158BINDING SITE FOR RESIDUE CL C 100
2AC2SOFTWARETHR A:158BINDING SITE FOR RESIDUE CL A 101
3AC3SOFTWAREASN C:133BINDING SITE FOR RESIDUE CL C 102
4AC4SOFTWAREALA A:130 , ASN A:133BINDING SITE FOR RESIDUE CL A 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SVF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SVF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SVF)

(-) Exons   (0, 0)

(no "Exon" information available for 1SVF)

(-) 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:64
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:64
                                   131       141       151       161       171       181    
             FUS_PIV5   122 TAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANC 185
               SCOP domains d1svfa_ A: Paramyxovirus sv5 fusion protein core                 SCOP domains
               CATH domains 1svfA00 A:122-185  [code=1.20.5.300, no name defined]            CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1svf A 122 TAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAANY 185
                                   131       141       151       161       171       181    


Chain B from PDB  Type:PROTEIN  Length:38
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:38
                                   449       459       469        
             FUS_PIV5   440 QILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAI 477
               SCOP domains d1svfb_ B:                             SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 1svf B 440 QILSIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAI 477
                                   449       459       469        


Chain C from PDB  Type:PROTEIN  Length:62
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:62
                                   131       141       151       161       171       181  
             FUS_PIV5   122 TAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAA 183
               SCOP domains d1svfc_ C: Paramyxovirus sv5 fusion protein core               SCOP domains
               CATH domains 1svfC00 C:122-183  [code=1.20.5.300, no name defined]          CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 1svf C 122 TAAVALVKANENAAAILNLKNAIQKTNAAVADVVQATQSLGTAVQAVQDHINSVVSPAITAA 183
                                   131       141       151       161       171       181  


Chain D from PDB  Type:PROTEIN  Length:35
 aligned with FUS_PIV5 | P04849 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:35
                                   452       462       472     
             FUS_PIV5   443 SIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAI 477
               SCOP domains d1svfd_ D:                          SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1svf D 443 SIDPLDISQNLAAVNKSLSDALQHLAQSDTYLSAI 477
                                   452       462       472
   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, 4)

Asymmetric Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SVF)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FUS_PIV5 | P04849)
biological process
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0006948    induction by virus of host cell-cell fusion    The process of syncytia-forming cell-cell fusion, caused by a virus.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    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:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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 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
    CL  [ 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 1svf)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  1svf
    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
  FUS_PIV5 | P04849
    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
  FUS_PIV5 | P04849
    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
        FUS_PIV5 | P04849: 2b9b 4gip 4wsg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SVF)