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(-) Description

Title :  CRYSTAL STRUCTURE OF E-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH SLEX
 
Authors :  W. S. Somers, R. T. Camphausen
Date :  13 Oct 00  (Deposition) - 13 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Lectin, Egf, Adhesion Molecule, Slex, Immune System, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. S. Somers, J. Tang, G. D. Shaw, R. T. Camphausen
Insights Into The Molecular Basis Of Leukocyte Tethering And Rolling Revealed By Structures Of P- And E-Selectin Bound To Sle(X) And Psgl-1.
Cell(Cambridge, Mass. ) V. 103 467 2000
PubMed-ID: 11081633  |  Reference-DOI: 10.1016/S0092-8674(00)00138-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E-SELECTIN
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CellOVARY [CHO] CELLS
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    Expression System Vector TypePLASMID
    FragmentLECTIN/EGF DOMAINS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDOTHELIAL LEUKOCYTE ADHESION MOLECULE 1, ELAM-1, LEUKOCYTE-ENDOTHELIAL CELL ADHESION MOLECULE 2, LECAM2, CD62E

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4MAG1Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:48 , ARG A:97 , GLU A:98 , HOH A:329 , GAL A:602BINDING SITE FOR RESIDUE SIA A 601
2AC2SOFTWAREGLU A:92 , TYR A:94 , ARG A:97 , ASN A:105 , GLU A:107 , HOH A:326 , SIA A:601 , MAG A:603 , FUC A:604BINDING SITE FOR RESIDUE GAL A 602
3AC3SOFTWAREGAL A:602 , FUC A:604BINDING SITE FOR RESIDUE MAG A 603
4AC4SOFTWAREGLU A:80 , ASN A:82 , ASN A:83 , ASN A:105 , ASP A:106 , GLU A:107 , CA A:160 , GAL A:602 , MAG A:603BINDING SITE FOR RESIDUE FUC A 604
5AC5SOFTWAREGLU A:80 , ASN A:82 , ASN A:83 , ASN A:105 , ASP A:106 , FUC A:604BINDING SITE FOR RESIDUE CA A 160

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:117
2A:90 -A:109
3A:122 -A:133
4A:127 -A:142
5A:144 -A:153

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014301M31ILYAM2_HUMANPolymorphism3917408AM10I
2UniProtVAR_011790C130WLYAM2_HUMANPolymorphism5360AC109W
3UniProtVAR_004191S149RLYAM2_HUMANPolymorphism5361AS128R

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

(-) PROSITE Motifs  (5, 4)

Asymmetric/Biological Unit (5, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.LYAM2_HUMAN111-138  1A:90-117
2EGF_3PS50026 EGF-like domain profile.LYAM2_HUMAN139-175  1A:118-154
3EGF_1PS00022 EGF-like domain signature 1.LYAM2_HUMAN163-174  1A:142-153
4EGF_2PS01186 EGF-like domain signature 2.LYAM2_HUMAN163-174  1A:142-153
5SUSHIPS50923 Sushi/CCP/SCR domain profile.LYAM2_HUMAN178-239
240-301
315-364
378-427
441-490
491-549
  1A:157-157
-
-
-
-
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003333601bENSE00001950222chr1:169703203-16970311292LYAM2_HUMAN-00--
1.2aENST000003333602aENSE00001367867chr1:169702801-16970271785LYAM2_HUMAN1-13130--
1.3aENST000003333603aENSE00000814463chr1:169702139-169701756384LYAM2_HUMAN13-1411291A:1-120120
1.4aENST000003333604aENSE00000789645chr1:169701083-169700976108LYAM2_HUMAN141-177371A:120-15637
1.5ENST000003333605ENSE00000789644chr1:169699758-169699573186LYAM2_HUMAN177-239631A:156-1572
1.6ENST000003333606ENSE00000451012chr1:169698814-169698629186LYAM2_HUMAN239-301630--
1.7ENST000003333607ENSE00000789642chr1:169698515-169698327189LYAM2_HUMAN301-364640--
1.8ENST000003333608ENSE00000789641chr1:169697387-169697199189LYAM2_HUMAN364-427640--
1.9ENST000003333609ENSE00000451027chr1:169697068-169696880189LYAM2_HUMAN427-490640--
1.10ENST0000033336010ENSE00000789639chr1:169696666-169696490177LYAM2_HUMAN490-549600--
1.11ENST0000033336011ENSE00000451043chr1:169695947-169695840108LYAM2_HUMAN549-585370--
1.12ENST0000033336012ENSE00000789637chr1:169695069-16969504822LYAM2_HUMAN585-59280--
1.13ENST0000033336013ENSE00000814464chr1:169694942-16969487073LYAM2_HUMAN592-610190--
1.14aENST0000033336014aENSE00000814465chr1:169693650-1696917821869LYAM2_HUMAN-00--

(-) 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:157
 aligned with LYAM2_HUMAN | P16581 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:157
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
          LYAM2_HUMAN    22 WSYNTSTEAMTYDEASAYCQQRYTHLVAIQNKEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNNRQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTAACTNTSCSGHGECVETINNYTCKCDPGFSGLKCEQIV 178
               SCOP domains d1g1ta1 A:1-118 E-selectin, C-lectin domain                                                                           d1g1ta2 A:119-157                       SCOP domains
               CATH domains 1g1tA01 A:1-119 Mannose-Binding Protein A, subunit A                                                                   1g1tA02 A:120-157 Laminin              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh.ee....hhhhhhhhhhhh......eee.eeee..eeee...........................eeee..........eeee......eeeeee.....hhhhh.eeeeee..eeeeee...ee.....ee. Sec.struct. author
                 SAPs(SNPs) ---------I--------------------------------------------------------------------------------------------------W------------------R----------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------C_TYPE_LECTIN_1             EGF_3  PDB: A:118-154                --S PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_2       ---- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------EGF_1       ---- PROSITE (3)
           Transcript 1 (1) Exon 1.3a  PDB: A:1-120 UniProt: 13-141 [INCOMPLETE]                                                                    -----------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------Exon 1.4a  PDB: A:120-156            - Transcript 1 (2)
                 1g1t A   1 WSYNTSTEAMTYDEASAYCQQRYTHLVAIQNKEEIEYLNSILSYSPSYYWIGIRKVNNVWVWVGTQKPLTEEAKNWAPGEPNNRQKDEDCVEIYIKREKDVGMWNDERCSKKKLALCYTAACTNTSCSGHGECVETINNYTCKCDPGFSGLKCEQIV 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G1T)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYAM2_HUMAN | P16581)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0070492    oligosaccharide binding    Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0043274    phospholipase binding    Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
    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:0033691    sialic acid binding    Interacting selectively and non-covalently with sialic acid, any of a variety of N- or O- substituted derivatives of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0030029    actin filament-based process    Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0019722    calcium-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
    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:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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: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:0050901    leukocyte tethering or rolling    Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
cellular component
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0030863    cortical cytoskeleton    The portion of the cytoskeleton that lies just beneath the plasma membrane.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, 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
        LYAM2_HUMAN | P165811esl 1kja 4c16 4csy

(-) Related Entries Specified in the PDB File

1g1q CRYSTAL STRUCTURE OF P-SELECTIN LECTIN/EGF DOMAINS
1g1r CRYSTAL STRUCTURE OF P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH SLEX
1g1s CRYSTAL STRUCTURE OF P-SELECTIN LECTIN/EGF DOMAINS