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- PDB-1qo3: Complex between NK cell receptor Ly49A and its MHC class I ligand... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qo3 | ||||||
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Title | Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd | ||||||
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![]() | RECEPTOR/IMMUNE SYSTEM / COMPLEX (NK RECEPTOR-MHC CLASS I) / NK CELL / INHIBITORY RECEPTOR / MHC-I / C-TYPE LECTIN-LIKE / HISTOCOMPATIBILITY / B2M / LY49 / LY-49 / RECEPTOR-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / signaling receptor activity / iron ion transport / T cell differentiation in thymus / protein refolding / carbohydrate binding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / viral protein processing / cell adhesion / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tormo, J. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Crystal Structure of a Lectin-Like Natural Killer Cell Receptor Bound to its Mhc Class I Ligand Authors: Tormo, J. / Natarajan, K. / Margulies, D.H. / Mariuzza, R.A. #1: Journal: Immunity / Year: 1999 Title: Interaction of the Nk Cell Inhibitory Receptor Ly49A with H-2Dd: Identification of a Site Distinct from the Tcr Site. Authors: Natarajan, K. / Boyd, L.F. / Schuck, P. / Yokoyama, W.M. / Eliat, D. / Margulies, D.H. #2: ![]() Title: Three-Dimensional Structure of H-2Dd Complexed with an Immunodominant Peptide from Human Immunodeficiency Virus Envelope Glycoprotein 120 Authors: Li, H. / Natarajan, K. / Malchiodi, E.L. / Margulies, D.H. / Mariuzza, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.5 KB | Display | ![]() |
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PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409 KB | Display | ![]() |
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Full document | ![]() | 415.2 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | BIOLOGICAL_UNIT: PROTEIN-PROTEIN COMPLEX BETWEEN THE NK-CELL SURFACE GLYCOPROTEIN DIMERIC AND THE HETEROTRIMER CONSISTING OF THE H-2DD HEAVY CHAIN, THE BETA-2-MICROGLOBULIN AND THE HIV ENVELOPE PEPTIDE. THERE IS A SECOND COMPLEX FORMED THROUGH SITE 2, AS DESCRIBED IN THE MAIN REFERENCE, AND CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. |
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Components
-Protein , 3 types, 4 molecules ABCD
#1: Protein | Mass: 32265.902 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11791.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 15921.329 Da / Num. of mol.: 2 / Fragment: C-TYPE LECTIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules P
#4: Protein/peptide | Mass: 1075.265 Da / Num. of mol.: 1 / Fragment: RESIDUES 318-327 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 2 types, 355 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | NATURAL VARIANTS ARISE FROM STRAIN C57BL/6 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Ly49A NKD : H-2Dd = 1.5:1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 33230 / % possible obs: 94.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.053 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 2.3→2.35 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.161 / % possible all: 80.7 |
Reflection | *PLUS Num. measured all: 128909 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 80.7 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 6.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1B6E, 1DDH Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28 Å2 / ksol: 0.340658 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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