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(-) Description

Title :  INTEGRIN EGF-LIKE MODULE 3 FROM THE BETA-2 SUBUNIT
 
Authors :  N. Beglova, S. C. Blacklow, J. Takagi, T. A. Springer
Date :  03 Mar 02  (Deposition) - 01 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Integrin, Beta-2 Subunit, Cell Adhesion, Cysteine-Rich Module, Egf-Like Module (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Beglova, S. C. Blacklow, J. Takagi, T. A. Springer
Cysteine-Rich Module Structure Reveals A Fulcrum For Integrin Rearrangement Upon Activation.
Nat. Struct. Biol. V. 9 282 2002
PubMed-ID: 11896403  |  Reference-DOI: 10.1038/NSB779
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTEGRIN BETA-2:CYSTEINE-RICH MODULE 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 535-574
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELL SURFACE ADHESION GLYCOPROTEINS LFA- 1/CR3/P150,95, CD18, BETA-SUBUNIT, COMPLEMENT RECEPTOR C3 BETA-SUBUNIT

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1L3Y)

(-) Sites  (0, 0)

(no "Site" information available for 1L3Y)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:2 -A:25
2A:7 -A:23
3A:15 -A:28
4A:30 -A:39

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L3Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L3Y)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_1PS00022 EGF-like domain signature 1.ITB2_HUMAN470-481
562-573
  1-
A:28-39
2EGF_2PS01186 EGF-like domain signature 2.ITB2_HUMAN470-483
562-575
601-615
  1-
A:28-40
-
3INTEGRIN_BETAPS00243 Integrins beta chain cysteine-rich domain signature.ITB2_HUMAN506-519
549-564
590-603
  1-
A:15-30
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5ENST000003978575ENSE00001530495chr21:46331375-4633129185ITB2_HUMAN-00--
1.7bENST000003978577bENSE00002161928chr21:46330700-4633064061ITB2_HUMAN1-20200--
1.7iENST000003978577iENSE00002166383chr21:46330287-4633019989ITB2_HUMAN20-49300--
1.10cENST0000039785710cENSE00001050919chr21:46327010-46326830181ITB2_HUMAN50-110610--
1.11eENST0000039785711eENSE00002202060chr21:46323450-46323280171ITB2_HUMAN110-167580--
1.12bENST0000039785712bENSE00001050930chr21:46321648-46321407242ITB2_HUMAN167-247810--
1.13ENST0000039785713ENSE00001314546chr21:46320390-46320235156ITB2_HUMAN248-299520--
1.14ENST0000039785714ENSE00002181070chr21:46319077-4631898296ITB2_HUMAN300-331320--
1.15aENST0000039785715aENSE00001280312chr21:46314975-4631488690ITB2_HUMAN332-361300--
1.15dENST0000039785715dENSE00001280354chr21:46313459-46313319141ITB2_HUMAN362-408470--
1.16ENST0000039785716ENSE00001280307chr21:46311911-46311724188ITB2_HUMAN409-471630--
1.17ENST0000039785717ENSE00001280195chr21:46310137-46309893245ITB2_HUMAN471-553831A:1-1919
1.18ENST0000039785718ENSE00001280299chr21:46309410-46309191220ITB2_HUMAN553-626741A:19-4123
1.19bENST0000039785719bENSE00001050945chr21:46308810-46308608203ITB2_HUMAN626-694690--
1.20ENST0000039785720ENSE00001280183chr21:46306817-46306651167ITB2_HUMAN694-749560--
1.21cENST0000039785721cENSE00001280374chr21:46306345-46305868478ITB2_HUMAN750-769200--

(-) 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:41
 aligned with ITB2_HUMAN | P05107 from UniProtKB/Swiss-Prot  Length:769

    Alignment length:41
                                   544       554       564       574 
           ITB2_HUMAN   535 ECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQC 575
               SCOP domains d1l3ya_ A: Integrin beta EGF-like domains SCOP domains
               CATH domains 1l3yA00 A:1-41 Laminin                    CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhheeee..eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------EGF_1       -- PROSITE (1)
                PROSITE (2) ---------------------------EGF_2          PROSITE (2)
                PROSITE (3) --------------INTEGRIN_BETA   ----------- PROSITE (3)
           Transcript 1 (1) Exon 1.17          ---------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.18  PDB: A:19-41 Transcript 1 (2)
                 1l3y A   1 ECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQA  41
                                    10        20        30        40 

   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

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L3Y)

(-) Gene Ontology  (46, 46)

NMR Structure(hide GO term definitions)
Chain A   (ITB2_HUMAN | P05107)
molecular function
    GO:0030369    ICAM-3 receptor activity    Combining with ICAM-3, intercellular adhesion molecule 3, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. ICAM-3, or CD50, are constitutively expressed on monocytes, granulocytes and lymphocytes; on physiological stimulation, they become transiently phosphorylated on serine residues.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    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:0071404    cellular response to low-density lipoprotein particle stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low-density lipoprotein particle stimulus.
    GO:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0043542    endothelial cell migration    The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0002523    leukocyte migration involved in inflammatory response    The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response.
    GO:0030101    natural killer cell activation    The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
    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:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    GO:0031623    receptor internalization    A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0050730    regulation of peptidyl-tyrosine phosphorylation    Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0034142    toll-like receptor 4 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
cellular component
    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:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    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:0034687    integrin alphaL-beta2 complex    An integrin complex that comprises one alphaL subunit and one beta2 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: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: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:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITB2_HUMAN | P051071jx3 1yuk 2jf1 2p26 2p28 2v7d 3k6s 3k71 3k72 4neh 4nen 5e6r 5e6s 5e6u 5e6v 5e6w 5e6x 5es4

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