[English] 日本語
Yorodumi- PDB-1qo3: Complex between NK cell receptor Ly49A and its MHC class I ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qo3 | ||||||
---|---|---|---|---|---|---|---|
Title | Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd | ||||||
Components |
| ||||||
Keywords | 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 | Function and homology information 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 / peptide binding / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / 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 / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / viral protein processing / cell adhesion / immune response / external side of plasma membrane / fusion of virus membrane with host plasma membrane / lysosomal 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 / apoptotic process / 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 | MUS MUSCULUS (house mouse) HUMAN IMMUNODEFICIENCY VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tormo, J. / Mariuzza, R.A. | ||||||
Citation | Journal: Nature / Year: 1999 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: Journal: J.Mol.Biol. / Year: 1999 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qo3.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qo3.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qo3_validation.pdf.gz | 409 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qo3_full_validation.pdf.gz | 415.2 KB | Display | |
Data in XML | 1qo3_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 1qo3_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qo3 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qo3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
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. |
-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.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Gene: H-2D / Plasmid: PET3A / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900 |
---|---|
#2: Protein | Mass: 11791.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: C57BL/6 / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Plasmid: PET21D / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 |
#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.) MUS MUSCULUS (house mouse) / Strain: C57BL/6 / Cell: NATURAL KILLER CELLS SOME T CELLS / Cellular location: CELL SURFACE / Plasmid: PET21A / Cellular location (production host): INCLUSION BODY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20937 |
-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.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: P04582 |
---|
-Non-polymers , 2 types, 355 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | NATURAL VARIANTS ARISE FROM STRAIN C57BL/6 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 28 Å2 / ksol: 0.340658 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|