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

(-) Description

Authors :  M. Yoneyama, T. Tomizawa, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 May 05  (Deposition) - 02 Nov 05  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta Ig-H3, Cell Adhesion Protein, Extracellular Matrix Protein, Integrin-Interacting Motif, Fas1 Domain, Fasciclin, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. Yoneyama, T. Tomizawa, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Fas1 Domain Of Human Transforming Growth Factor-Beta Induced Protein Ig-H3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    Expression System PlasmidP040524-06
    Expression System Vector TypePLASMID
    FragmentFAS1 DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1X3B)

(-) Sites  (0, 0)

(no "Site" information available for 1X3B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (24, 24)

NMR Structure (24, 24)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_005079P501TBGH3_HUMANDisease (CDL3A)121909212AG7T
02UniProtVAR_031535V505DBGH3_HUMANDisease (CDL1)  ---AV11D
03UniProtVAR_031536L509RBGH3_HUMANDisease (EBMD)121909216AL15R
04UniProtVAR_012446L518PBGH3_HUMANDisease (CDL1)  ---AL24P
05UniProtVAR_018484L518RBGH3_HUMANDisease (CDL1)  ---AL24R
06UniProtVAR_005080L527RBGH3_HUMANDisease (CDL1)  ---AL33R
07UniProtVAR_018485T538RBGH3_HUMANDisease (CDL1)  ---AT44R
08UniProtVAR_031537V539DBGH3_HUMANUnclassified  ---AV45D
09UniProtVAR_031538F540SBGH3_HUMANDisease (CDL3A)121909214AF46S
11UniProtVAR_031539A546DBGH3_HUMANDisease (CDL1)267607109AA52D
12UniProtVAR_012448A546TBGH3_HUMANDisease (CDL3A)  ---AA52T
13UniProtVAR_031540P551QBGH3_HUMANDisease (CDL1)267607110AP57Q
14UniProtVAR_005082R555QBGH3_HUMANDisease (CDTB)121909209AR61Q
15UniProtVAR_005083R555WBGH3_HUMANDisease (CDGG1)121909208AR61W
16UniProtVAR_031541L569RBGH3_HUMANDisease (CDL1)  ---AL75R
17UniProtVAR_031543H572RBGH3_HUMANDisease (CDL1)  ---AH78R
18UniProtVAR_031544G594VBGH3_HUMANUnclassified  ---AG100V
19UniProtVAR_012449N622HBGH3_HUMANUnclassified  ---AN128H
20UniProtVAR_018486N622KBGH3_HUMANDisease (CDL3A)  ---AN128K
21UniProtVAR_018487G623DBGH3_HUMANDisease (CDL1)121909215AG129D
22UniProtVAR_018488H626PBGH3_HUMANDisease (CDL1)  ---AH132P
23UniProtVAR_012450H626RBGH3_HUMANDisease (CDL1)  ---AH132R
24UniProtVAR_018489V631DBGH3_HUMANUnclassified  ---AV137D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1FAS1PS50213 FAS1/BIgH3 domain profile.BGH3_HUMAN103-236

(-) Exons   (0, 0)

(no "Exon" information available for 1X3B)

(-) 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:146
 aligned with BGH3_HUMAN | Q15582 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:158
                                   495       505       515       525       535       545       555       565       575       585       595       605       615       625       635        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------Fasciclin-1x3bA01 A:19-140                                                                                                --------- Pfam domains
         Sec.struct. author Sec.struct. author
             SAPs(SNPs) (1) ---------------T---D---R--------P--------R----------RDS---S-D----Q---Q-------------R--R---------------------V---------------------------HD--P----D------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------R---------------------------T--------W------------------------------------------------------------------K---R----------------- SAPs(SNPs) (2)
                    PROSITE FAS1  PDB: - ---FAS1  PDB: A:8-138 UniProt: 502-632                                                                                                ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                               |     -   |    11        21        31        41        51        61        71        81        91       101       111       121       131       141|  | | |
                               4         5                                                                                                                                      142  | | |
                                                                                                                                                                                   143 | |
                                                                                                                                                                                     145 |

   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 1X3B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X3B)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (BGH3_HUMAN | Q15582)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.


(-) 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)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(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 1x3b)
(no "Sites" information available for 1x3b)
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x3b)

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    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
  BGH3_HUMAN | Q15582
    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)
    Disease InformationOMIM
    Disease InformationOMIM
    Disease InformationOMIM
    Disease InformationOMIM
    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
  BGH3_HUMAN | Q15582
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        BGH3_HUMAN | Q155822ltb 2ltc 2vxp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X3B)