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
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)

(-) Description

Title :  THE SECRET DOMAIN FROM ECTROMELIA VIRUS
 
Authors :  X. Q. Wang, X. G. Xue, D. L. Wang
Date :  28 Aug 10  (Deposition) - 17 Aug 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Sandwich, Viral Tnf Receptor, Chemokine-Binding Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. G. Xue, Q. Y. Lu, H. Wei, D. L. Wang, D. W. Chen, G. J. He, L. Huang, H. Z. Wang, X. Q. Wang
Structural Basis Of Chemokine Sequestration By Crmd, A Poxvirus-Encoded Tumor Necrosis Factor Receptor
Plos Pathog. V. 7 02162 2011
PubMed-ID: 21829356  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002162

(-) Compounds

Molecule 1 - TUMOUR NECROSIS FACTOR RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SECRET DOMAIN, UNP RESIDUES 162-320
    Gene: CRMD
    Organism Scientific: ECTROMELIA VIRUS
    Organism Taxid: 12643

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ON9)

(-) Sites  (0, 0)

(no "Site" information available for 3ON9)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:180 -A:317
2A:204 -A:238
3A:246 -A:276
4B:180 -B:317
5B:204 -B:238
6B:246 -B:276

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:173 -Pro A:174
2Tyr B:173 -Pro B:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ON9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ON9)

(-) Exons   (0, 0)

(no "Exon" information available for 3ON9)

(-) 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:160
 aligned with Q7TDW8_9POXV | Q7TDW8 from UniProtKB/TrEMBL  Length:320

    Alignment length:176
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
         Q7TDW8_9POXV   145 GDVICKKCPGNIDKCDLSFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVDKLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCLSNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCERD 320
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------...eeeeeeeee.......eee...eeeee...eeeeeeee.....eeeeeeeee..eeeeeeee............eeeeeeee.....eee............eeeeeee.....eeeeeeeee....hhhhheeeeee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on9 A 161 G----------------SFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVDKLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCLSNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCERD 320
                            |        -       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
                            |              162                                                                                                                                                              
                          161                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with Q7TDW8_9POXV | Q7TDW8 from UniProtKB/TrEMBL  Length:320

    Alignment length:176
                                   154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
         Q7TDW8_9POXV   145 GDVICKKCPGNIDKCDLSFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVDKLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCLSNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCERD 320
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------...eeeeeeeee.......eee...eeeee...eeeeeeee.....eeeeeeeee..eeeeeeee............eeeeeeee.....eee............eeeeeee.....eeeeeeeee....hhhhheeeeee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3on9 B 161 G----------------SFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVDKLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCLSNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCERD 320
                            |        -       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
                          161              162
   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 3ON9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ON9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ON9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7TDW8_9POXV | Q7TDW8)
molecular function
    GO:0005031    tumor necrosis factor-activated receptor activity    Combining with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages, to initiate a change in cell function.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.

 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 3on9)
 
  Sites
(no "Sites" information available for 3on9)
 
  Cis Peptide Bonds
    Tyr A:173 - Pro A:174   [ RasMol ]  
    Tyr B:173 - Pro B:174   [ RasMol ]  
 
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 | Biol. Unit 1 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
  3on9
    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
  Q7TDW8_9POXV | Q7TDW8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q7TDW8_9POXV | Q7TDW8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q7TDW8_9POXV | Q7TDW8: 3ona

(-) Related Entries Specified in the PDB File

3ona