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(-) Description

Title :  STRUCTURE OF THE INTEGRIN BETA3 (A711P,K716A) TRANSMEMBRANE SEGMENT
 
Authors :  T. Schmidt, T. S. Ulmer
Date :  27 Jan 11  (Deposition) - 21 Dec 11  (Release) - 25 Jan 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
NMR Structure *:  A  (1x)
Keywords :  Transmembrane Segment, Integrin, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kim, T. Schmidt, E. G. Cho, F. Ye, T. S. Ulmer, M. H. Ginsberg
Basic Amino-Acid Side Chains Regulate Transmembrane Integri Signalling.
Nature V. 481 209 2012
PubMed-ID: 22178926  |  Reference-DOI: 10.1038/NATURE10697

(-) Compounds

Molecule 1 - INTEGRIN BETA-3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET44
    FragmentSEQUENCE DATABASE RESIDUES 711-753
    GeneITGB3, GP3A
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLATELET MEMBRANE GLYCOPROTEIN IIIA, GPIIIA

 Structural Features

(-) Chains, Units

  1
NMR Structure (21x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L91)

(-) Sites  (0, 0)

(no "Site" information available for 2L91)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L91)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L91)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069924D749HITB3_HUMANDisease (BDPLT16)398122372AD723H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069924D749HITB3_HUMANDisease (BDPLT16)398122372AD723H

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2L91)

(-) Exons   (0, 0)

(no "Exon" information available for 2L91)

(-) 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:43
 aligned with ITB3_HUMAN | P05106 from UniProtKB/Swiss-Prot  Length:788

    Alignment length:43
                                   720       730       740       750   
           ITB3_HUMAN   711 PECPKGPDILVVLLSVMGAILLIGLAALLIWKLLITIHDRKEF 753
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------H---- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2l91 A 685 PESPKGPDILVVLLSVMGAILLIGLAPLLIWALLITIHDRKEF 727
                                   694       704       714       724   

   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 2L91)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L91)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L91)

(-) Gene Ontology  (76, 76)

NMR Structure(hide GO term definitions)
Chain A   (ITB3_HUMAN | P05106)
molecular function
    GO:0019960    C-X3-C chemokine binding    Interacting selectively and non-covalently with a C-X3-C chemokine; C-X3-C chemokines have three amino acids between the first two cysteines of the characteristic four-cysteine motif.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0015026    coreceptor activity    Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0017134    fibroblast growth factor binding    Interacting selectively and non-covalently with a fibroblast growth factor.
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0031994    insulin-like growth factor I binding    Interacting selectively and non-covalently with insulin-like growth factor I.
    GO:0038132    neuregulin binding    Interacting selectively and non-covalently with a neuregulin, a member of the EGF family of growth factors.
    GO:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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).
    GO:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0043184    vascular endothelial growth factor receptor 2 binding    Interacting selectively and non-covalently with vascular endothelial growth factor receptor 2.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    GO:0060055    angiogenesis involved in wound healing    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0038027    apolipoprotein A-I-mediated signaling pathway    A series of molecular signals initiated by the binding of apolipoprotein A-I to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    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:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0031589    cell-substrate adhesion    The attachment of a cell to the underlying substrate via adhesion molecules.
    GO:0007044    cell-substrate junction assembly    The aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate.
    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:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0048333    mesodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell.
    GO:0050919    negative chemotaxis    The directed movement of a motile cell or organism towards a lower concentration of a chemical.
    GO:0010888    negative regulation of lipid storage    Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0032369    negative regulation of lipid transport    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050748    negative regulation of lipoprotein metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids.
    GO:0045715    negative regulation of low-density lipoprotein particle receptor biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of low-density lipoprotein particle receptors.
    GO:0010745    negative regulation of macrophage derived foam cell differentiation    Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    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:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0045124    regulation of bone resorption    Any process that modulates the frequency, rate or extent of bone tissue loss (resorption).
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0014909    smooth muscle cell migration    The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
    GO:0035295    tube development    The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0035867    alphav-beta3 integrin-IGF-1-IGF1R complex    A protein complex that consists of an alphav-beta3 integrin complex bound to insulin-like growth factor-1 (IGF-1) and type I insulin-like growth factor receptor (IGF1R). IGF1R is a heterotetramer that consists of two alpha-subunits and two beta-subunits.
    GO:0071062    alphav-beta3 integrin-vitronectin complex    A protein complex that consists of an alphav-beta3 integrin complex bound to vitronectin.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0031527    filopodium membrane    The portion of the plasma membrane surrounding a filopodium.
    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:0034683    integrin alphav-beta3 complex    An integrin complex that comprises one alphav subunit and one beta3 subunit.
    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:0031258    lamellipodium membrane    The portion of the plasma membrane surrounding a lamellipodium.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031528    microvillus membrane    The portion of the plasma membrane surrounding a microvillus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITB3_HUMAN | P051061jv2 1kup 1kuz 1l5g 1m1x 1m8o 1miz 1mk7 1mk9 1rn0 1s4x 1tye 1u8c 2h7d 2h7e 2ini 2k9j 2knc 2kv9 2l1c 2ljd 2lje 2ljf 2mtp 2n9y 2q6w 2rmz 2rn0 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 3fcs 3fcu 3ije 3nid 3nif 3nig 3t3m 3t3p 3zdx 3zdy 3zdz 3ze0 3ze1 3ze2 4cak 4g1e 4g1m 4hxj 4mmx 4mmy 4mmz 4o02 4z7n 4z7o 4z7q 5hdb

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