+Open data
-Basic information
Entry | Database: PDB / ID: 3cii | ||||||
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Title | Structure of NKG2A/CD94 bound to HLA-E | ||||||
Components |
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Keywords | IMMUNE SYSTEM / C-type lectin-like / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Lectin / Receptor / Signal-anchor | ||||||
Function / homology | Function and homology information natural killer cell mediated immunity / inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway ...natural killer cell mediated immunity / inhibitory MHC class Ib receptor activity / CD8-positive, gamma-delta intraepithelial T cell differentiation / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / natural killer cell inhibitory signaling pathway / peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell tolerance induction / protein antigen binding / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of regulatory T cell differentiation / positive regulation of endothelial cell apoptotic process / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / filopodium membrane / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / positive regulation of macrophage cytokine production / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / protein homotrimerization / stimulatory C-type lectin receptor signaling pathway / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of interleukin-4 production / MHC class I protein binding / cellular defense response / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / positive regulation of interleukin-12 production / T cell receptor binding / negative regulation of angiogenesis / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.41 Å | ||||||
Authors | Strong, R.K. / Kaiser, B.K. / Pizarro, J.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structural basis for NKG2A/CD94 recognition of HLA-E. Authors: Kaiser, B.K. / Pizarro, J.C. / Kerns, J. / Strong, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cii.cif.gz | 244.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cii.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 3cii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cii ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cii | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 31640.803 Da / Num. of mol.: 2 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1048.321 Da / Num. of mol.: 2 / Fragment: peptide presented by HLA-E (UNP residues 3-11) / Source method: obtained synthetically Details: peptide is naturally found in humans and was chemically synthesized. References: UniProt: P17693 #4: Protein | Mass: 14213.664 Da / Num. of mol.: 2 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLRD1, CD94 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q13241 #5: Protein | Mass: 13754.549 Da / Num. of mol.: 2 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLRC1, NKG2A / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P26715 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.95 Å3/Da / Density % sol: 79.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8M ammonium sulfate, 0.3-0.7% sucrose, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 4.41→70 Å / Num. obs: 22619 / % possible obs: 100 % / Redundancy: 34.4 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 4.4→4.56 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.03 / Num. unique all: 2189 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KPR, 1B6E Resolution: 4.41→67.88 Å / Cor.coef. Fo:Fc: 0.753 / Cor.coef. Fo:Fc free: 0.68 / SU B: 136.822 / SU ML: 0.792 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.161 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.41→67.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 4.405→4.52 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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