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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALPHA-X BETA2 INTEGRIN I DOMAIN
 
Authors :  T. Vorup-Jensen, C. Ostermeier, M. Shimaoka, U. Hommel, T. A. Springer
Date :  30 Oct 02  (Deposition) - 18 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Rossmann Fold, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Vorup-Jensen, C. Ostermeier, M. Shimaoka, U. Hommel, T. A. Springer
Structure And Allosteric Regulation Of The Alpha X Beta 2 Integrin I Domain.
Proc. Natl. Acad. Sci. Usa V. 100 1873 2003
PubMed-ID: 12554829  |  Reference-DOI: 10.1073/PNAS.0237387100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-X
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentI DOMAIN
    GeneITGAX OR CD11C
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUKOCYTE ADHESION GLYCOPROTEIN P150,95 ALPHA CHAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N3Y)

(-) Sites  (0, 0)

(no "Site" information available for 1N3Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N3Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:164 -Pro A:165
2Lys A:288 -Pro A:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049632F201LITAX_HUMANPolymorphism1574566AF182L
2UniProtVAR_031925A251TITAX_HUMANPolymorphism2230428AA232T

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITAX_HUMAN151-329  1A:132-310

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002682961ENSE00002161727chr16:31366509-31366612104ITAX_HUMAN1-13130--
1.2ENST000002682962ENSE00001700348chr16:31367214-31367319106ITAX_HUMAN13-48360--
1.3ENST000002682963ENSE00001655758chr16:31367946-31368049104ITAX_HUMAN48-83360--
1.4ENST000002682964ENSE00001765995chr16:31368352-3136842271ITAX_HUMAN83-106240--
1.5ENST000002682965ENSE00001738489chr16:31368574-31368685112ITAX_HUMAN107-144380--
1.6ENST000002682966ENSE00001681517chr16:31371021-31371151131ITAX_HUMAN144-187441A:129-16840
1.7ENST000002682967ENSE00001787655chr16:31371241-31371386146ITAX_HUMAN188-236491A:169-21749
1.8ENST000002682968ENSE00001794926chr16:31371631-31371784154ITAX_HUMAN236-287521A:217-26852
1.9ENST000002682969ENSE00001772645chr16:31372384-31372534151ITAX_HUMAN288-338511A:269-31749
1.10ENST0000026829610ENSE00001761178chr16:31373157-3137323074ITAX_HUMAN338-362250--
1.11ENST0000026829611ENSE00001770549chr16:31373396-31373525130ITAX_HUMAN363-406440--
1.12ENST0000026829612ENSE00001689564chr16:31373932-31374074143ITAX_HUMAN406-453480--
1.13ENST0000026829613ENSE00001631428chr16:31374256-31374396141ITAX_HUMAN454-500470--
1.14ENST0000026829614ENSE00001773966chr16:31374486-31374695210ITAX_HUMAN501-570700--
1.15ENST0000026829615ENSE00001786232chr16:31382405-31382535131ITAX_HUMAN571-614440--
1.16ENST0000026829616ENSE00001778190chr16:31382655-31382818164ITAX_HUMAN614-669560--
1.17ENST0000026829617ENSE00001724430chr16:31382951-31383105155ITAX_HUMAN669-720520--
1.18ENST0000026829618ENSE00001660734chr16:31383699-31383830132ITAX_HUMAN721-764440--
1.19ENST0000026829619ENSE00001665346chr16:31383918-3138399174ITAX_HUMAN765-789250--
1.20ENST0000026829620ENSE00000944391chr16:31384570-31384711142ITAX_HUMAN789-836480--
1.21ENST0000026829621ENSE00001361752chr16:31388120-31388236117ITAX_HUMAN837-875390--
1.22ENST0000026829622ENSE00000944393chr16:31388321-3138840080ITAX_HUMAN876-902270--
1.23ENST0000026829623ENSE00000944394chr16:31388503-3138858684ITAX_HUMAN902-930290--
1.24ENST0000026829624ENSE00000944395chr16:31390889-3139096779ITAX_HUMAN930-956270--
1.25ENST0000026829625ENSE00000944396chr16:31391078-31391185108ITAX_HUMAN957-992360--
1.26ENST0000026829626ENSE00000944397chr16:31391303-3139138684ITAX_HUMAN993-1020280--
1.27ENST0000026829627ENSE00001698612chr16:31391587-31391700114ITAX_HUMAN1021-1058380--
1.28ENST0000026829628ENSE00001662024chr16:31391844-31391945102ITAX_HUMAN1059-1092340--
1.29ENST0000026829629ENSE00000944400chr16:31392218-31392328111ITAX_HUMAN1093-1129370--
1.30ENST0000026829630ENSE00001389530chr16:31393124-313943181195ITAX_HUMAN1130-1163340--

(-) 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:189
 aligned with ITAX_HUMAN | P20702 from UniProtKB/Swiss-Prot  Length:1163

    Alignment length:189
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327         
           ITAX_HUMAN   148 QEQDIVFLIDGSGSISSRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQTHFTFEEFRRSSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDSLDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIASKPSQEHIFKVEDFDALKDIQNQLKEKIFAI 336
               SCOP domains d1n3ya_ A: Integrin alpha-x beta2                                                                                                                                                             SCOP domains
               CATH domains 1n3yA00 A:129-317  [code=3.40.50.410, no name defined]                                                                                                                                        CATH domains
               Pfam domains ---VWA-1n3yA01 A:132-310                                                                                                                                                              ------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhhhhhhh......eeeeeeee...eeeeehhhhhhhh.hhhhhhh.........hhhhhhhhhhh...hhhhh.....eeeeeeee.........hhhhhhhhhhhh..eeeeeee.hhhhh..hhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------L-------------------------------------------------T------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---VWFA  PDB: A:132-310 UniProt: 151-329                                                                                                                                              ------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:129-168 [INCOMPLETE]   Exon 1.7  PDB: A:169-217 UniProt: 188-236        ---------------------------------------------------Exon 1.9  PDB: A:269-317 UniProt: 288-338         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.8  PDB: A:217-268 UniProt: 236-287           ------------------------------------------------- Transcript 1 (2)
                 1n3y A 129 QEQDIVFLIDGSGSISSRNFATMMNFVRAVISQFQRPSTQFSLMQFSNKFQTHFTFEEFRRSSNPLSLLASVHQLQGFTYTATAIQNVVHRLFHASYGARRDAAKILIVITDGKKEGDSLDYKDVIPMADAAGIIRYAIGVGLAFQNRNSWKELNDIASKPSQEHIFKVEDFDALKDIQNQLKEKIFAI 317
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308         

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ITAX_HUMAN | P20702)
molecular function
    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).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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: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:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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.

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    Arg A:164 - Pro A:165   [ RasMol ]  
    Lys A:288 - Pro A:289   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITAX_HUMAN | P207022luv 3k6s 3k71 3k72 4neh 4nen 5es4

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