Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NMR STRUCTURE OF DOMAIN III OF THE WEST NILE VIRUS ENVELOPE PROTEIN, STRAIN 385-99
 
Authors :  D. E. Volk, D. W. Beasley, D. A. Kallick, M. R. Holbrook, A. D. Barrett, D. G. Gorenstein
Date :  26 Jan 04  (Deposition) - 06 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
NMR Structure *:  A  (1x)
Keywords :  Beta Barrel, Flavivirus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Volk, D. W. Beasley, D. A. Kallick, M. R. Holbrook, A. D. Barrett, D. G. Gorenstein
Solution Structure And Antibody Binding Studies Of The Envelope Protein Domain Iii From The New York Strain Of Wes Nile Virus
J. Biol. Chem. V. 279 38755 2004
PubMed-ID: 15190071  |  Reference-DOI: 10.1074/JBC.M402385200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL C2X
    Expression System StrainC2X
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDOMAIN III
    Organism ScientificWEST NILE VIRUS
    Organism Taxid307044
    Strain385-99

 Structural Features

(-) Chains, Units

  1
NMR Structure (15x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1S6N)

(-) Sites  (0, 0)

(no "Site" information available for 1S6N)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:14 -A:45

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S6N)

(-) Exons   (0, 0)

(no "Exon" information available for 1S6N)

(-) Sequences/Alignments

NMR Structure
   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:115
 aligned with Q913C7_WNV | Q913C7 from UniProtKB/TrEMBL  Length:426

    Alignment length:115
                                   301       311       321       331       341       351       361       371       381       391       401     
           Q913C7_WNV   292 MEKLQLKGTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIGK 406
               SCOP domains d1s6na_ A: Envelope glycoprotein                                                                                    SCOP domains
               CATH domains 1s6nA00 A:1-115  [code=2.60.40.350, no name defined]                                                                CATH domains
               Pfam domains -----Fla-Flavi_glycop_C-1s6nA01 A:10-108                                                                    ------- Pfam domains
         Sec.struct. author .................eeeeeeeee.....eeeeeee..........eeee..........ee..............eeeeeee...eeeeeeeee..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1s6n A   1 ISEFQLKGTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIGK 115
                                    10        20        30        40        50        60        70        80        90       100       110     

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

NMR Structure

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (Q913C7_WNV | Q913C7)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.
    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:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
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: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:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    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

NMR Structure
  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 1s6n)
 
  Sites
(no "Sites" information available for 1s6n)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1s6n)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1s6n
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q913C7_WNV | Q913C7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q913C7_WNV | Q913C7
    Protein Disorder PredictionDisEMBL | 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 1S6N)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1S6N)