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(-) Description

Title :  N-GLYCAN AND POLYPEPTIDE NMR SOLUTION STRUCTURES OF THE ADHESION DOMAIN OF HUMAN CD2
 
Authors :  D. F. Wyss, J. S. Choi, G. Wagner
Date :  26 May 95  (Deposition) - 08 Nov 96  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (18x)
NMR Structure *:  A  (1x)
Keywords :  Cell Surface Adhesion Receptor, Immunoglobulin Superfamily V-Set Domain, T Lymphocyte Adhesion Glycoprotein, Adhesion Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. F. Wyss, J. S. Choi, J. Li, M. H. Knoppers, K. J. Willis, A. R. Arulanandam, A. Smolyar, E. L. Reinherz, G. Wagner
Conformation And Function Of The N-Linked Glycan In The Adhesion Domain Of Human Cd2.
Science V. 269 1273 1995
PubMed-ID: 7544493
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN CD2
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CommonCHINESE HAMSTER
    Expression System GeneSCD2182
    Expression System PlasmidPM1
    Expression System Taxid10029
    FragmentADHESION DOMAIN
    GeneSCD2182
    OrganOVARY
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsGLYCOSYLATED
    Other Details - SourceTHE ADHESION DOMAIN OF HUMAN CD2 (HSCD2105) WAS OBTAINED BY CLOSTRIPAIN DIGESTION OF THE TWO-DOMAIN HUMAN CD2 (HSCD2182)
    SynonymHSCD2105

 Structural Features

(-) Chains, Units

  1
NMR Structure (18x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

NMR Structure (3, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
NMR Structure * (3, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

NMR Structure (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:65 , THR A:67 , NAG A:107BINDING SITE FOR RESIDUE NAG A 106
2AC2SOFTWARENAG A:106 , BMA A:108BINDING SITE FOR RESIDUE NAG A 107
3AC3SOFTWARENAG A:107 , MAN A:109 , MAN A:111BINDING SITE FOR RESIDUE BMA A 108
4AC4SOFTWAREBMA A:108 , MAN A:110BINDING SITE FOR RESIDUE MAN A 109
5AC5SOFTWAREMAN A:109BINDING SITE FOR RESIDUE MAN A 110
6AC6SOFTWAREBMA A:108 , MAN A:112 , MAN A:113BINDING SITE FOR RESIDUE MAN A 111
7AC7SOFTWARELYS A:71 , MAN A:111BINDING SITE FOR RESIDUE MAN A 112
8AC8SOFTWAREMAN A:111 , MAN A:114BINDING SITE FOR RESIDUE MAN A 113
9AC9SOFTWAREMAN A:113BINDING SITE FOR RESIDUE MAN A 114

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GYA)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003694781aENSE00001450130chr1:117297007-117297175169CD2_HUMAN1-21210--
1.2aENST000003694782aENSE00000785006chr1:117297253-117297573321CD2_HUMAN21-1281081A:1-104104
1.3ENST000003694783ENSE00000785007chr1:117303024-117303254231CD2_HUMAN128-205781A:104-1052
1.4ENST000003694784ENSE00000785008chr1:117307106-117307228123CD2_HUMAN205-246420--
1.5ENST000003694785ENSE00001141790chr1:117311086-117311850765CD2_HUMAN246-3511060--

(-) 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:105
 aligned with CD2_HUMAN | P06729 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:105
                                    34        44        54        64        74        84        94       104       114       124     
            CD2_HUMAN    25 KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 129
               SCOP domains d1gyaa_ A: CD2, first domain                                                                              SCOP domains
               CATH domains 1gyaA00 A:1-105 Immunoglobulins                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee...eeeee...........eeeeee.....eeeee..hhheee....eeee...eeeee........eeeeeee.......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-104 UniProt: 21-128 [INCOMPLETE]                                                    - Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 1gya A   1 KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTYKLFKNGTLKIKHLKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQER 105
                                    10        20        30        40        50        60        70        80        90       100     

   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 1GYA)

(-) Gene Ontology  (28, 28)

NMR Structure(hide GO term definitions)
Chain A   (CD2_HUMAN | P06729)
molecular function
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    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:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0034113    heterotypic cell-cell adhesion    The attachment of a cell to a cell of a different type via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0001766    membrane raft polarization    The clustering and aggregation of membrane rafts at a single cellular pole during activation of particular cell types, such as lymphocytes.
    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:1902715    positive regulation of interferon-gamma secretion    Any process that activates or increases the frequency, rate or extent of interferon-gamma secretion.
    GO:2000484    positive regulation of interleukin-8 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-8 secretion.
    GO:0030887    positive regulation of myeloid dendritic cell activation    Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0045580    regulation of T cell differentiation    Any process that modulates the frequency, rate or extent of T cell differentiation.
    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.
cellular component
    GO:0046658    anchored component of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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
        CD2_HUMAN | P067291cdb 1hnf 1l2z 1qa9 2j6o 2j7i

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