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Yorodumi- PDB-1qqd: CRYSTAL STRUCTURE OF HLA-CW4, A LIGAND FOR THE KIR2D NATURAL KILL... -
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-Basic information
Entry | Database: PDB / ID: 1qqd | ||||||
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Title | CRYSTAL STRUCTURE OF HLA-CW4, A LIGAND FOR THE KIR2D NATURAL KILLER CELL INHIBITORY RECEPTOR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN (IG)-LIKE DOMAIN / ALPHA HELIX / BETA SHEET | ||||||
Function / homology | Function and homology information TAP binding / secretory granule membrane / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...TAP binding / secretory granule membrane / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Fan, Q.R. / Wiley, D.C. | ||||||
Citation | Journal: J.Exp.Med. / Year: 1999 Title: Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor Authors: Fan, Q.R. / Wiley, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qqd.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqd.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qqd_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 1qqd_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1qqd_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 1qqd_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqd ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31830.947 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30504, UniProt: P10321*PLUS |
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#2: Protein | Mass: 11676.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1115.213 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The nonameric peptide contains the consensus peptide-binding motif for HLA-Cw4, which was determined by pool sequencing. |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, calcium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: seeding using 12% PEG8000, 0.2 M Ca acetate, and 0.1M Na cacodylate | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: May 31, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→22 Å / Num. all: 12895 / Num. obs: 12895 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 60.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.504 / Num. unique all: 1175 / % possible all: 90.5 |
Reflection shell | *PLUS % possible obs: 90.5 % |
-Processing
Software |
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Refinement | Resolution: 2.7→22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2295736.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.12 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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