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(-) Description

Title :  I DOMAIN FROM HUMAN INTEGRIN ALPHA1-BETA1
 
Authors :  Y. Nymalm, J. S. Puranen, T. K. M. Nyholm, J. Kapyla, H. Kidron, O. Pentik T. T. Airenne, J. Heino, J. P. Slotte, M. S. Johnson, T. A. Salminen
Date :  23 Jun 03  (Deposition) - 13 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Integrin, Alpha1, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nymalm, J. S. Puranen, T. K. M. Nyholm, J. Kapyla, H. Kidron, T. T. Airenne, J. Heino, J. P. Slotte, M. S. Johnson, T. A. Salminen
Jararhagin-Derived Rkkh Peptides Induce Structural Changes In Alpha1I Domain Of Human Integrin Alpha1Beta1.
J. Biol. Chem. V. 279 7962 2004
PubMed-ID: 14660600  |  Reference-DOI: 10.1074/JBC.M312912200

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-3
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUE 136-338
    GeneITGA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLAMININ AND COLLAGEN RECEPTOR, VLA-1, CD49A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:152 , SER A:154 , ASP A:253 , HOH A:603 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWARESER B:152 , SER B:154 , ASP B:253 , HOH B:604 , HOH B:605 , HOH B:606BINDING SITE FOR RESIDUE MG B 500
3AC3SOFTWAREGLU A:232 , ARG A:238 , ASN A:313 , VAL A:314 , SER A:315 , HOH A:697BINDING SITE FOR RESIDUE GOL A 602
4AC4SOFTWARELYS A:170 , ARG A:171 , ARG B:242 , GLY B:243 , VAL B:244 , GLU B:272 , ASN B:273 , HOH B:708BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PT6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:156 -Pro A:157
2Glu A:305 -Pro A:306
3Tyr B:156 -Pro B:157
4Glu B:305 -Pro B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PT6)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FG_GAPPS51470 FG-GAP repeat profile.ITA1_HUMAN30-91
101-160
365-417
476-538
422-475
557-615
619-679
  1-
-
B:337-337
-
-
-
-
2VWFAPS50234 VWFA domain profile.ITA1_HUMAN172-355
 
  2A:144-327
B:144-327
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FG_GAPPS51470 FG-GAP repeat profile.ITA1_HUMAN30-91
101-160
365-417
476-538
422-475
557-615
619-679
  0-
-
-
-
-
-
-
2VWFAPS50234 VWFA domain profile.ITA1_HUMAN172-355
 
  1A:144-327
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FG_GAPPS51470 FG-GAP repeat profile.ITA1_HUMAN30-91
101-160
365-417
476-538
422-475
557-615
619-679
  1-
-
B:337-337
-
-
-
-
2VWFAPS50234 VWFA domain profile.ITA1_HUMAN172-355
 
  1-
B:144-327

(-) Exons   (5, 9)

Asymmetric Unit (5, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002825881aENSE00002078767chr5:52083730-52084248519ITA1_HUMAN1-21210--
1.3ENST000002825883ENSE00001006625chr5:52145199-52145319121ITA1_HUMAN21-61410--
1.4ENST000002825884ENSE00001145956chr5:52157281-52157393113ITA1_HUMAN61-99390--
1.6ENST000002825886ENSE00001006627chr5:52160597-5216068589ITA1_HUMAN99-128300--
1.7ENST000002825887ENSE00001006615chr5:52160805-52160916112ITA1_HUMAN129-166380--
1.8ENST000002825888ENSE00001006626chr5:52161524-52161651128ITA1_HUMAN166-208432A:142-180
B:143-180
39
38
1.10ENST0000028258810ENSE00001006605chr5:52177705-52177853149ITA1_HUMAN209-258502A:181-230
B:181-230
50
50
1.12bENST0000028258812bENSE00001006634chr5:52183647-52183797151ITA1_HUMAN258-308512A:230-280
B:230-280
51
51
1.13ENST0000028258813ENSE00001006613chr5:52189506-52189671166ITA1_HUMAN309-364562A:281-333
B:281-336
53
56
1.14ENST0000028258814ENSE00001006632chr5:52193286-5219335974ITA1_HUMAN364-388251-
B:336-337
-
2
1.15ENST0000028258815ENSE00001006633chr5:52194069-52194213145ITA1_HUMAN389-437490--
1.16bENST0000028258816bENSE00001006619chr5:52201593-52201738146ITA1_HUMAN437-485490--
1.17ENST0000028258817ENSE00001006608chr5:52204728-52204871144ITA1_HUMAN486-533480--
1.18ENST0000028258818ENSE00001006611chr5:52205992-52206249258ITA1_HUMAN534-619860--
1.19ENST0000028258819ENSE00001006624chr5:52211294-52211424131ITA1_HUMAN620-663440--
1.20ENST0000028258820ENSE00001006604chr5:52214562-52214728167ITA1_HUMAN663-719570--
1.21ENST0000028258821ENSE00001006621chr5:52216162-52216298137ITA1_HUMAN719-764460--
1.22ENST0000028258822ENSE00001006614chr5:52218607-52218717111ITA1_HUMAN765-801370--
1.23ENST0000028258823ENSE00001006620chr5:52221108-52221317210ITA1_HUMAN802-871700--
1.24ENST0000028258824ENSE00001006609chr5:52223414-5222349481ITA1_HUMAN872-898270--
1.25ENST0000028258825ENSE00001006612chr5:52225455-5222553177ITA1_HUMAN899-924260--
1.26bENST0000028258826bENSE00001006623chr5:52227877-5222796690ITA1_HUMAN924-954310--
1.26cENST0000028258826cENSE00001006622chr5:52229724-52229826103ITA1_HUMAN954-988350--
1.27ENST0000028258827ENSE00001006631chr5:52233231-52233344114ITA1_HUMAN989-1026380--
1.28ENST0000028258828ENSE00001006618chr5:52235420-52235521102ITA1_HUMAN1027-1060340--
1.29ENST0000028258829ENSE00001006617chr5:52235670-52235774105ITA1_HUMAN1061-1095350--
1.30ENST0000028258830ENSE00001006630chr5:52240773-5224086593ITA1_HUMAN1096-1126310--
1.31ENST0000028258831ENSE00001006607chr5:52243175-52243291117ITA1_HUMAN1127-1165390--
1.32cENST0000028258832cENSE00001006629chr5:52248237-522523274091ITA1_HUMAN1166-1179140--

(-) Sequences/Alignments

Asymmetric 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:192
 aligned with ITA1_HUMAN | P56199 from UniProtKB/Swiss-Prot  Length:1179

    Alignment length:192
                                   179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359  
           ITA1_HUMAN   170 QLDIVIVLDGSNSIYPWDSVTAFLNDLLERMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERIFA 361
               SCOP domains d1pt6a_ A: Integrin alpha1-beta1                                                                                                                                                                 SCOP domains
               CATH domains 1pt6A00 A:142-333  [code=3.40.50.410, no name defined]                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......hhhhhhhhhhhhhh.........eeeeeee...eeeee......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.....eeeeeeee......hhhhhhhhhhhhhh.eeeeeeeehhhhhhh...hhhhhhhhhhhh..hhhhheeee.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --VWFA  PDB: A:144-327 UniProt: 172-355                                                                                                                                                   ------ PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:142-180 [INCOMPLETE]  Exon 1.10  PDB: A:181-230 UniProt: 209-258        --------------------------------------------------Exon 1.13  PDB: A:281-333 UniProt: 309-364            Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.12b  PDB: A:230-280 UniProt: 258-308        ----------------------------------------------------- Transcript 1 (2)
                 1pt6 A 142 QLDIVIVLDGSNSIYPWDSVTAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGTDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERIFA 333
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with ITA1_HUMAN | P56199 from UniProtKB/Swiss-Prot  Length:1179

    Alignment length:195
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
           ITA1_HUMAN   171 LDIVIVLDGSNSIYPWDSVTAFLNDLLERMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERIFALEAT 365
               SCOP domains d1pt6b_ B: Integrin alpha1-beta1                                                                                                                                                                    SCOP domains
               CATH domains 1pt6B00 B:143-337  [code=3.40.50.410, no name defined]                                                                                                                                              CATH domains
           Pfam domains (1) -VWA-1pt6B01 B:144-327                                                                                                                                                                   ---------- Pfam domains (1)
           Pfam domains (2) -VWA-1pt6B02 B:144-327                                                                                                                                                                   ---------- Pfam domains (2)
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhh.........eeeeeee...eeeee......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh......eeeeeee.....hhhhhhhhhhhhhhh.eeeeeeeehhhhhhhh..hhhhhhhhhhhh..hhhhheeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -VWFA  PDB: B:144-327 UniProt: 172-355                                                                                                                                                   ---------F PROSITE
           Transcript 1 (1) Exon 1.8  PDB: B:143-180 [INCOMPLETE] Exon 1.10  PDB: B:181-230 UniProt: 209-258        --------------------------------------------------Exon 1.13  PDB: B:281-336 UniProt: 309-364              - Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.12b  PDB: B:230-280 UniProt: 258-308        -------------------------------------------------------1. Transcript 1 (2)
                 1pt6 B 143 LDIVIVLDGSNSIYPWDSVTAFLNDLLKRMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGTDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERIFALEAT 337
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)
1aVWA-1pt6B01B:144-327
1bVWA-1pt6B02B:144-327

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ITA1_HUMAN | P56199)
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:0098639    collagen binding involved in cell-matrix adhesion    Any collagen binding that occurs as part of cell-matrix adhesion.
    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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    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:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0045123    cellular extravasation    The migration of a leukocyte from the blood vessels into the surrounding tissue.
    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:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0043525    positive regulation of neuron apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:0042311    vasodilation    An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0045178    basal part of cell    The region of a cell situated near the base. For example, in a polarized epithelial cell, the basal surface rests on the basal lamina that separates the epithelium from other tissue.
    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:0034665    integrin alpha1-beta1 complex    An integrin complex that comprises one alpha1 subunit and one beta1 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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ITA1_HUMAN | P561991qc5 1qcy 2l8s 2m32 4a0q 5hgj

(-) Related Entries Specified in the PDB File

1qcy