Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
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

Title :  SOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE INTEGRIN ALPHA-IIB SUBUNIT
 
Authors :  O. Vinogradova, T. Haas, E. F. Plow, J. Qin
Date :  27 Dec 99  (Deposition) - 28 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (16x)
Keywords :  Helix-Turn, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Vinogradova, T. Haas, E. F. Plow, J. Qin
A Structural Basis For Integrin Activation By The Cytoplasmic Tail Of The Alpha Iib-Subunit.
Proc. Natl. Acad. Sci. Usa V. 97 1450 2000
PubMed-ID: 10677482  |  Reference-DOI: 10.1073/PNAS.040548197
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-IIB SUBUNIT
    ChainsA
    EngineeredYES
    FragmentCYTOPLASMIC DOMAIN
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF RESIDUES IS NATURALLY FOUND IN THE PLATELETS OF HOMO SAPIENS (HUMAN).
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (16x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1DPK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030468R1026QITA2B_HUMANDisease (GT)879255514AR7Q
2UniProtVAR_069919R1026WITA2B_HUMANDisease (BDPLT16)  ---AR7W

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002624071ENSE00000854286chr17:42466873-42466654220ITA2B_HUMAN1-63630--
1.2ENST000002624072ENSE00000390828chr17:42463499-42463378122ITA2B_HUMAN63-104420--
1.3ENST000002624073ENSE00000732018chr17:42463289-4246319298ITA2B_HUMAN104-136330--
1.4ENST000002624074ENSE00000732019chr17:42463084-42462919166ITA2B_HUMAN137-192560--
1.5ENST000002624075ENSE00001504857chr17:42462703-4246265450ITA2B_HUMAN192-208170--
1.6ENST000002624076ENSE00001504855chr17:42462577-4246253246ITA2B_HUMAN209-224160--
1.7ENST000002624077ENSE00000854285chr17:42462444-42462316129ITA2B_HUMAN224-267440--
1.8ENST000002624078ENSE00001504854chr17:42461953-4246190648ITA2B_HUMAN267-283170--
1.9ENST000002624079ENSE00000854284chr17:42461722-4246167944ITA2B_HUMAN283-297150--
1.10ENST0000026240710ENSE00000732026chr17:42461506-4246145354ITA2B_HUMAN298-315180--
1.11ENST0000026240711ENSE00000732027chr17:42461314-4246126253ITA2B_HUMAN316-333180--
1.12ENST0000026240712ENSE00000732028chr17:42461072-42460861212ITA2B_HUMAN333-404720--
1.13ENST0000026240713ENSE00000732030chr17:42458429-42458247183ITA2B_HUMAN404-465620--
1.14ENST0000026240714ENSE00000732031chr17:42458013-4245796846ITA2B_HUMAN465-480160--
1.15ENST0000026240715ENSE00000732032chr17:42457858-42457754105ITA2B_HUMAN480-515360--
1.16ENST0000026240716ENSE00000732033chr17:42457669-4245761456ITA2B_HUMAN515-534200--
1.17ENST0000026240717ENSE00000732034chr17:42457521-42457370152ITA2B_HUMAN534-584510--
1.18ENST0000026240718ENSE00000732036chr17:42457182-42457057126ITA2B_HUMAN585-626420--
1.19ENST0000026240719ENSE00000732038chr17:42456078-4245601168ITA2B_HUMAN627-649230--
1.20ENST0000026240720ENSE00000732040chr17:42455877-42455730148ITA2B_HUMAN649-698500--
1.21ENST0000026240721ENSE00000732042chr17:42455158-4245506693ITA2B_HUMAN699-729310--
1.22ENST0000026240722ENSE00000732043chr17:42454456-4245437780ITA2B_HUMAN730-756270--
1.23ENST0000026240723ENSE00000732044chr17:42453756-4245367681ITA2B_HUMAN756-783280--
1.24ENST0000026240724ENSE00000732045chr17:42453552-42453453100ITA2B_HUMAN783-816340--
1.25ENST0000026240725ENSE00000732046chr17:42453353-42453201153ITA2B_HUMAN817-867510--
1.26aENST0000026240726aENSE00000732047chr17:42453084-42452959126ITA2B_HUMAN868-909420--
1.27ENST0000026240727ENSE00000732049chr17:42452479-42452366114ITA2B_HUMAN910-947380--
1.28ENST0000026240728ENSE00001321776chr17:42452128-42452027102ITA2B_HUMAN948-981340--
1.29ENST0000026240729ENSE00000854277chr17:42451838-42451722117ITA2B_HUMAN982-1020391A:1-11
1.30ENST0000026240730ENSE00000854276chr17:42449791-42449550242ITA2B_HUMAN1021-1039191A:2-2019

(-) 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:20
 aligned with ITA2B_HUMAN | P08514 from UniProtKB/Swiss-Prot  Length:1039

    Alignment length:20
                                  1029      1039
         ITA2B_HUMAN   1020 KVGFFKRNRPPLEEDDEEGE 1039
               SCOP domains d1dpka_ A:           SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .......hhhhhh....... Sec.struct. author
             SAPs(SNPs) (1) ------Q------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------W------------- SAPs(SNPs) (2)
                    PROSITE -------------------- PROSITE
               Transcript 1 1Exon 1.30           Transcript 1
                1dpk A    1 KVGFFKRNRPPLEEDDEEGE   20
                                    10        20

   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
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DPK)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (ITA2B_HUMAN | P08514)
molecular function
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0070051    fibrinogen binding    Interacting selectively and non-covalently with fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    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:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0002687    positive regulation of leukocyte migration    Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0008305    integrin complex    A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0031092    platelet alpha granule membrane    The lipid bilayer surrounding the platelet alpha granule.

 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 1dpk)
 
  Sites
(no "Sites" information available for 1dpk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dpk)
 

(-) 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
  1dpk
    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
  ITA2B_HUMAN | P08514
    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)
  187800
    Disease InformationOMIM
  273800
    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
  ITA2B_HUMAN | P08514
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ITA2B_HUMAN | P085141dpq 1jx5 1kup 1kuz 1m8o 1rn0 1s4w 1tye 1uv9 2k1a 2k9j 2knc 2mtp 2n9y 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 3fcs 3fcu 3nid 3nif 3nig 3t3m 3t3p 3zdx 3zdy 3zdz 3ze0 3ze1 3ze2 4cak 4z7n 4z7o 4z7q 5hdb

(-) Related Entries Specified in the PDB File

1dpq SOLUTION STRUCTURE OF THE CONSTITUTIVELY ACTIVE MUTANT OF THE INTEGRIN ALPHA IIB CYTOPLASMIC DOMAIN.