Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF VACCINA VIRUS H7 PROTEIN DISPLAYS A NOVEL PHOSPHOINOSITIDE BINDING FOLD REQUIRED FOR MEMBRANE BIOGENESIS
 
Authors :  S. Kolli, X. Meng, X. Wu, D. Shengjuler, C. E. Cameron, Y. Xiang, J. Deng
Date :  19 Aug 14  (Deposition) - 31 Dec 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Phophoinositide Binding, Pi3P Pi4P, Poxvirus, Membrane Biogenesis, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kolli, X. Meng, X. Wu, D. Shengjuler, C. E. Cameron, Y. Xiang, J. Deng
Structure-Function Analysis Of Vaccinia Virus H7 Protein Reveals A Novel Phosphoinositide Binding Fold Essential For Poxvirus Replication.
J. Virol. V. 89 2209 2015
PubMed-ID: 25473060  |  Reference-DOI: 10.1128/JVI.03073-14

(-) Compounds

Molecule 1 - LATE PROTEIN H7
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VACWR105, H7R
    Organism Common: VACV
    Organism Scientific: VACCINIA VIRUS
    Organism Taxid: 10254
    Strain: WESTERN RESERVE
    Synonym: PROTEIN H8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4W60)

(-) Sites  (0, 0)

(no "Site" information available for 4W60)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:76 -C:76
2B:76 -D:76

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W60)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W60)

(-) Exons   (0, 0)

(no "Exon" information available for 4W60)

(-) 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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh......hhhhhhhhhhhhhh....eeeeee.....eeeeee....hhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4w60 A   1 MEMDKRMKSLAMTAFFGELSTLDIMALIMSIFKRHPNNTIFSVDKDGQFMIDFEYDNYKASQYLDLTLTPISGDECKTHASSIAEQLASVDIIKEDISEYIKTTPRLKRFIKKYRNR 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh......hhhhhhhhhhhhhh....eeeeee.....eeeeee....hhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4w60 B   1 MEMDKRMKSLAMTAFFGELSTLDIMALIMSIFKRHPNNTIFSVDKDGQFMIDFEYDNYKASQYLDLTLTPISGDECKTHASSIAEQLASVDIIKEDISEYIKTTPRLKRFIKKYRN 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh......hhhhhhhhhhhhhh....eeeeee.....eeeeee....hhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4w60 C   1 MEMDKRMKSLAMTAFFGELSTLDIMALIMSIFKRHPNNTIFSVDKDGQFMIDFEYDNYKASQYLDLTLTPISGDECKTHASSIAEQLASVDIIKEDISEYIKTTPRLKRFIKKYRN 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain D from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhhhhhhhhhh....eeeeee.....eeeeee....hhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4w60 D   3 MDKRMKSLAMTAFFGELSTLDIMALIMSIFKRHPNNTIFSVDKDGQFMIDFEYDNYKASQYLDLTLTPISGDECKTHASSIAEQLASVDIIKEDISEYIKTTPRLKRFIKKYRN 116
                                    12        22        32        42        52        62        72        82        92       102       112
   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 4W60)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W60)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W60)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 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
(no "Ligands, Modified Residues, Ions" information available for 4w60)
 
  Sites
(no "Sites" information available for 4w60)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4w60)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4w60
    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
  H7_VACCW | P08586
    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
  H7_VACCW | P08586
    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
        H7_VACCW | P08586: 4w5x

(-) Related Entries Specified in the PDB File

4w5x 4w60