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(-) Description

Title :  CRYSTAL STRUCTURE OF DOMAINS 3 & 4 OF RAT CD4 AND THEIR RELATIONSHIP TO THE NH2-TERMINAL DOMAINS
 
Authors :  R. L. Brady, E. J. Dodson, G. Lange
Date :  28 Jan 93  (Deposition) - 15 Jul 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  T-Cell Surface Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. L. Brady, E. J. Dodson, G. G. Dodson, G. Lange, S. J. Davis, A. F. Williams, A. N. Barclay
Crystal Structure Of Domains 3 And 4 Of Rat Cd4: Relation To The Nh2-Terminal Domains.
Science V. 260 979 1993
PubMed-ID: 8493535
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T CELL SURFACE GLYCOPROTEIN CD4
    ChainsA
    EngineeredYES
    OrganOVARY
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 1CID)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:119 -A:161

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:61 -Pro A:62

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000219151ENSRNOE00000218100chr4:161014038-16101401821CD4_RAT-00--
1.2ENSRNOT000000219152ENSRNOE00000155314chr4:161006190-16100610487CD4_RAT1-19190--
1.3ENSRNOT000000219153ENSRNOE00000155435chr4:161005975-161005811165CD4_RAT19-74560--
1.4ENSRNOT000000219154ENSRNOE00000155527chr4:160996878-160996720159CD4_RAT74-127540--
1.5ENSRNOT000000219155ENSRNOE00000155620chr4:160995724-160995488237CD4_RAT127-206800--
1.6ENSRNOT000000219156ENSRNOE00000155706chr4:160993648-160993313336CD4_RAT206-3181131A:1-109109
1.7ENSRNOT000000219157ENSRNOE00000155795chr4:160990624-160990421204CD4_RAT318-386691A:109-17769
1.8ENSRNOT000000219158ENSRNOE00000155882chr4:160989880-160989762119CD4_RAT386-425401A:177-1771
1.9ENSRNOT000000219159ENSRNOE00000155973chr4:160989467-16098940068CD4_RAT426-448230--
1.10ENSRNOT0000002191510ENSRNOE00000156068chr4:160988864-160988512353CD4_RAT448-457100--

(-) 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:177
 aligned with CD4_RAT | P05540 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:177
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       
              CD4_RAT   210 TSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEKAPSSQSWITFSLKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQEVNLVVMKVTQPDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLSEGEEVKMDSKIQV 386
               SCOP domains d1cida1 A:1-105 CD4 V-set domains                                                                        d1cida2 A:106-177 CD4 C2-set domains                                     SCOP domains
               CATH domains 1cidA01 A:1-106 Immunoglobulins                                                                           1cidA02 A:107-177 Immunoglobulins                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeee.........eeeeeeeee........eeeeeee..eeeee........ee......eeee...hhhh.eeeeeeee....eeeeeeeeeeeeee.....eeeeeee......eeeeeee....eeeee...eeeee.....eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:1-109 UniProt: 206-318 [INCOMPLETE]                                                         -------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:109-177 UniProt: 318-386                             Transcript 1 (2)
                 1cid A   1 TSITAYKSEGESAEFSFPLNLGEESLQGELRWKAEKAPSSQSWITFSLKNQKVSVQKSTSNPKFQLSETLPLTLQIPQVSLQFAGSGNLTLTLDRGILYQEVNLVVMKVTQPDSNTLTCEVMGPTSPKMRLILKQENQEARVSRQEKVIQVQAPEAGVWQCLLSEGEEVKMDSKIQV 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       

   Legend:   → Mismatch (orange background)
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  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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD4_RAT | P05540)
molecular function
    GO:0042289    MHC class II protein binding    Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0015026    coreceptor activity    Combining with an extracellular or intracellular messenger, and in cooperation with a nearby primary receptor, initiating a change in cell activity.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0019865    immunoglobulin binding    Interacting selectively and non-covalently with an immunoglobulin.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:1990782    protein tyrosine kinase binding    Interacting selectively and non-covalently with protein tyrosine kinase.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0045058    T cell selection    The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0035397    helper T cell enhancement of adaptive immune response    Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006948    induction by virus of host cell-cell fusion    The process of syncytia-forming cell-cell fusion, caused by a virus.
    GO:0032507    maintenance of protein location in cell    Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
    GO:0050870    positive regulation of T cell activation    Any process that activates or increases the frequency, rate or extent of T cell activation.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0010524    positive regulation of calcium ion transport into cytosol    Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components.
    GO:0050850    positive regulation of calcium-mediated signaling    Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0050863    regulation of T cell activation    Any process that modulates the frequency, rate or extent of T cell activation.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0033280    response to vitamin D    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 vitamin D stimulus.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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: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: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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