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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ECTODOMAIN OF HUMAN CD81 LARGE EXTRACELLULAR LOOP (HCD81-LEL)
 
Authors :  M. Zhang, S. Cui
Date :  14 Oct 14  (Deposition) - 01 Jul 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helical Bundle, Disulfide Bond, Immune Cell Adhesion, Morphology, Activation, Proliferation, Differentiation, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Yang, M. Zhang, X. Chi, X. Liu, B. Qin, S. Cui
An Intramolecular Bond At Cluster Of Differentiation 81 Ectodomain Is Important For Hepatitis C Virus Entry
Faseb J. 2015
PubMed-ID: 26116703  |  Reference-DOI: 10.1096/FJ.15-272880

(-) Compounds

Molecule 1 - CD81 ANTIGEN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLARGE EXTRACELLULAR LOOP, UNP RESIDUES 113-202
    GeneCD81, TAPA1, TSPAN28
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym26 KDA CELL SURFACE PROTEIN TAPA-1, TARGET OF THE ANTIPROLIFERATIVE ANTIBODY 1, TETRASPANIN-28, TSPAN-28

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:133 , ALA A:140 , ASN A:142 , ALA A:143 , HOH A:444 , HOH A:452BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREHOH A:410BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASN A:142 , ALA A:143BINDING SITE FOR RESIDUE MG A 303
4AC4SOFTWARELYS B:201 , HOH B:440BINDING SITE FOR RESIDUE MG B 301
5AC5SOFTWAREASN A:141 , HOH A:457 , HOH B:446 , HOH B:452BINDING SITE FOR RESIDUE MG B 302

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:156 -A:190
2A:157 -A:175
3B:156 -B:190
4B:157 -B:175

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3X0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X0E)

(-) Exons   (0, 0)

(no "Exon" information available for 3X0E)

(-) 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:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 3x0e A 113 FVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPSGSNIISNLFKEDCHQKIDDLFSGK 201
                                   122       132       142       152       162       172       182       192         

Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3x0e B 113 FVNKDQIAKDVKQFYDQALQQAVVDDDANNAKAVVKTFHETLDCCGSSTLTALTTSVLKNNLCPNIISNLFKEDCHQKIDDLFSGK 201
                                   122       132       142       152       162       172   ||  185       195      
                                                                                         176|                     
                                                                                          180                     

   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 3X0E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X0E)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3x0e)
 

(-) 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
  3x0e
    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
  CD81_HUMAN | P60033
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CD81_HUMAN | P60033
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CD81_HUMAN | P600331g8q 1iv5 2avz 5dfv 5dfw 5m2c 5m33 5m3d 5m3t 5m4r 5tcx

(-) Related Entries Specified in the PDB File

1g8q CRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN
1iv5 CRYSTAL STRUCTURE OF HUMAN CD81 EXTRACELLULAR DOMAIN
3x0f
3x0g