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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FREE HUMAN NKG2D IMMUNORECEPTOR
 
Authors :  B. J. Mcfarland, T. Kortemme, D. Baker, R. K. Strong
Date :  12 Sep 02  (Deposition) - 15 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  C-Type Lectin-Like Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. J. Mcfarland, T. Kortemme, S. F. Yu, D. Baker, R. K. Strong
Symmetry Recognizing Asymmetry: Analysis Of The Interaction Between The C-Type Lectin-Like Immunoreceptor Nkg2D And Mhc Class I-Like Ligands
Structure V. 11 411 2003
PubMed-ID: 12679019  |  Reference-DOI: 10.1016/S0969-2126(03)00047-9

(-) Compounds

Molecule 1 - NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B+
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 80-216
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNKG2-D ACTIVATING NK RECEPTOR, NK CELL RECEPTOR D

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:136 , ILE A:173 , SER A:175 , HOH A:303 , HOH A:340 , HOH A:365BINDING SITE FOR RESIDUE PO4 A 500

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:96 -A:105
2A:99 -A:110
3A:127 -A:211
4A:189 -A:203

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030738N177SNKG2D_HUMANPolymorphism2306182AN177S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030738N177SNKG2D_HUMANPolymorphism2306182AN177S

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.NKG2D_HUMAN106-212  1A:106-212
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.NKG2D_HUMAN106-212  2A:106-212

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002406181ENSE00001524992chr12:10542640-1054254299NKG2D_HUMAN-00--
1.2ENST000002406182ENSE00002198225chr12:10541474-10541370105NKG2D_HUMAN1-14140--
1.3ENST000002406183ENSE00001656271chr12:10539609-10539502108NKG2D_HUMAN14-50370--
1.4ENST000002406184ENSE00001160615chr12:10532391-1053229993NKG2D_HUMAN50-81320--
1.5ENST000002406185ENSE00001160608chr12:10532081-1053204636NKG2D_HUMAN81-93131A:88-936
1.6aENST000002406186aENSE00001160601chr12:10531304-10531153152NKG2D_HUMAN93-143511A:93-14351
1.7ENST000002406187ENSE00000821886chr12:10530834-10530731104NKG2D_HUMAN144-178351A:144-17835
1.8ENST000002406188ENSE00001160593chr12:10525830-10524953878NKG2D_HUMAN178-216391A:178-21538

(-) Sequences/Alignments

Asymmetric 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:128
 aligned with NKG2D_HUMAN | P26718 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:128
                                    97       107       117       127       137       147       157       167       177       187       197       207        
          NKG2D_HUMAN    88 QIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
               SCOP domains d1mpua_ A: NK cell-activating receptor nkg2d                                                                                     SCOP domains
               CATH domains 1mpuA00 A:88-215 Mannose-Binding Protein A, subunit A                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee....eeeeeeeeehhhhhhhhhhhh..ee........hhhhhhh..eeeeeeee......eee...........eee......eeeee...eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------S-------------------------------------- SAPs(SNPs)
                    PROSITE ------------------C_TYPE_LECTIN_2  PDB: A:106-212 UniProt: 106-212                                                           --- PROSITE
           Transcript 1 (1) 1.5   --------------------------------------------------Exon 1.7  PDB: A:144-178           ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.6a  PDB: A:93-143 UniProt: 93-143           ----------------------------------Exon 1.8  PDB: A:178-215 [INCOMPLETE]  Transcript 1 (2)
                 1mpu A  88 QIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                    97       107       117       127       137       147       157       167       177       187       197       207        

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A   (NKG2D_HUMAN | P26718)
molecular function
    GO:0042288    MHC class I protein binding    Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0032394    MHC class Ib receptor activity    Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families.
    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:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071222    cellular response to lipopolysaccharide    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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0034260    negative regulation of GTPase activity    Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
    GO:2000502    negative regulation of natural killer cell chemotaxis    Any process that stops, prevents or reduces the frequency, rate or extent of natural killer cell chemotaxis.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0030887    positive regulation of myeloid dendritic cell activation    Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation.
    GO:0045954    positive regulation of natural killer cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
    GO:0002860    positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target    Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated cytotoxicity directed against tumor cell target.
    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: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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    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: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
        NKG2D_HUMAN | P267181hyr 1kcg 4pdc 4s0u

(-) Related Entries Specified in the PDB File

1hq8 MOUSE NKG2D
1hyr HUMAN NKG2D IN COMPLEX WITH MIC-A
1jsk MOUSE NKG2D IN COMPLEX WITH RAE-1BETA
1kcg HUMAN NKG2D IN COMPLEX WITH ULBP3