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(-) Description

Title :  ALPHA-1 INTEGRIN I-DOMAIN IN COMPLEX WITH GLOGEN TRIPLE HELICAL PEPTIDE
 
Authors :  Y. Chin, S. Headey, B. Mohanty, P. Mcewan, J. Swarbrick, T. Mulhern, J. E J. Simpson, M. Scanlon
Date :  07 Jan 13  (Deposition) - 06 Nov 13  (Release) - 12 Feb 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (10x)
NMR Structure *:  A,B,C,D  (1x)
Keywords :  Alpha-1 Integrin, I-Domain, Glogen, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. K. Chin, S. J. Headey, B. Mohanty, R. Patil, P. A. Mcewan, J. D. Swarbrick, T. D. Mulhern, J. Emsley, J. S. Simpson, M. J. Scanlon
The Structure Of Integrin Alpha 1I Domain In Complex With A Collagen-Mimetic Peptide.
J. Biol. Chem. V. 288 36796 2013
PubMed-ID: 24187131  |  Reference-DOI: 10.1074/JBC.M113.480251

(-) Compounds

Molecule 1 - INTEGRIN ALPHA-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET28A+
    GeneITGA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD49 ANTIGEN-LIKE FAMILY MEMBER A, LAMININ AND COLLAGEN RECEPTOR, VLA-1
 
Molecule 2 - GLOGEN PEPTIDE
    ChainsB, C, D
    EngineeredYES
    Other DetailsSYNTHETICALLY OBTAINED
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
NMR Structure (10x)ABCD
NMR Structure * (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

NMR Structure (4, 25)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2HYP18Mod. Amino Acid4-HYDROXYPROLINE
3MG1Ligand/IonMAGNESIUM ION
4NH23Mod. Amino AcidAMINO GROUP
NMR Structure * (3, 24)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2HYP18Mod. Amino Acid4-HYDROXYPROLINE
3MG-1Ligand/IonMAGNESIUM ION
4NH23Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:13 , SER A:15 , THR A:81 , GLU C:212BINDING SITE FOR RESIDUE MG A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M32)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M32)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M32)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITA1_HUMAN172-355  1A:5-188
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITA1_HUMAN172-355  1A:5-188

(-) Exons   (4, 4)

NMR Structure (4, 4)
 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_HUMAN166-208431A:1-4141
1.10ENST0000028258810ENSE00001006605chr5:52177705-52177853149ITA1_HUMAN209-258501A:42-9150
1.12bENST0000028258812bENSE00001006634chr5:52183647-52183797151ITA1_HUMAN258-308511A:91-14151
1.13ENST0000028258813ENSE00001006613chr5:52189506-52189671166ITA1_HUMAN309-364561A:142-19251
1.14ENST0000028258814ENSE00001006632chr5:52193286-5219335974ITA1_HUMAN364-388250--
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

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

    Alignment length:192
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357  
           ITA1_HUMAN   168 STQLDIVIVLDGSNSIYPWDSVTAFLNDLLERMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERI 359
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.......hhhhhhhhhhhhhhh.......eeeeeee...eee........hhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhh......eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhhh....hhhh.eee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----VWFA  PDB: A:5-188 UniProt: 172-355                                                                                                                                                     ---- PROSITE
           Transcript 1 (1) Exon 1.8  PDB: A:1-41 UniProt: 166-208   Exon 1.10  PDB: A:42-91 UniProt: 209-258          --------------------------------------------------Exon 1.13  PDB: A:142-192 UniProt: 309-364          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.12b  PDB: A:91-141 UniProt: 258-308         --------------------------------------------------- Transcript 1 (2)
                 2m32 A   1 STQLDIVIVLDGSNSIYPWDSVTAFLNDLLERMDIGPKQTQVGIVQYGENVTHEFNLNKYSSTEEVLVAAKKIVQRGGRQTMTALGIDTARKEAFTEARGARRGVKKVMVIVTDGESHDNHRLKKVIQDCEDENIQRFSIAILGSYNRGNLSTEKFVEEIKSIASEPTEKHFFNVSDELALVTIVKTLGERI 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  

Chain B from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ....................... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 2m32 B 101 xGPpGPpGLpGENGPpGPpGPpx 123
                            |  |  |110     | 120 ||
                          101-ACE |  |     |  |  ||
                             104-HYP |     |  |  ||
                                107-HYP    |  |  ||
                                   110-HYP |  |  ||
                                         116-HYP ||
                                            119-HYP
                                               122-HYP
                                                123-NH2

Chain C from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ....................... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 2m32 C 201 xGPpGPpGLpGENGPpGPpGPpx 223
                            |  |  |210     | 220 ||
                            |  |  |  |     |  |  ||
                          201-ACE |  |     |  |  ||
                             204-HYP |     |  |  ||
                                207-HYP    |  |  ||
                                   210-HYP |  |  ||
                                         216-HYP ||
                                            219-HYP
                                               222-HYP
                                                223-NH2

Chain D from PDB  Type:PROTEIN  Length:23
                                                       
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ....................... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 2m32 D 301 xGPpGPpGLpGENGPpGPpGPpx 323
                            |  |  |310     | 320 ||
                            |  |  |  |     |  |  ||
                          301-ACE |  |     |  |  ||
                             304-HYP |     |  |  ||
                                307-HYP    |  |  ||
                                   310-HYP |  |  ||
                                         316-HYP ||
                                            319-HYP
                                               322-HYP
                                                323-NH2

   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 2M32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M32)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M32)

(-) Gene Ontology  (35, 35)

NMR Structure(hide GO term definitions)
Chain A   (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 | P561991pt6 1qc5 1qcy 2l8s 4a0q 5hgj

(-) Related Entries Specified in the PDB File

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