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Yorodumi- PDB-6pag: Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA... -
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-Basic information
Entry | Database: PDB / ID: 6pag | ||||||
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Title | Killer cell immunoglobulin-like receptor 2DL3 in complex with HLA-C*07:02 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / KIR receptor / HLA / innate immunity / NK cell / T cell | ||||||
Function / homology | Function and homology information Chromatin modifying enzymes / epigenetic regulation of gene expression / TAP 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 / antigen binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...Chromatin modifying enzymes / epigenetic regulation of gene expression / TAP 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 / antigen binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / secretory granule membrane / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / PRC2 methylates histones and DNA / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Defective pyroptosis / HDACs deacetylate histones / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / RNA Polymerase I Promoter Escape / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / response to molecule of bacterial origin / HDMs demethylate histones / 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 / PKMTs methylate histone lysines / antigen processing and presentation of endogenous peptide antigen via MHC class I / RMTs methylate histone arginines / positive regulation of T cell cytokine production / Meiotic recombination / MHC class I protein complex / Pre-NOTCH Transcription and Translation / nucleosome assembly / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / nucleosome / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / signaling receptor activity / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / positive regulation of protein binding / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / ER-Phagosome pathway / iron ion transport / Senescence-Associated Secretory Phenotype (SASP) / protein refolding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Moradi, S. / Rossjohn, J. / Vivian, J.P. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural plasticity of KIR2DL2 and KIR2DL3 enables altered docking geometries atop HLA-C. Authors: Moradi, S. / Stankovic, S. / O'Connor, G.M. / Pymm, P. / MacLachlan, B.J. / Faoro, C. / Retiere, C. / Sullivan, L.C. / Saunders, P.M. / Widjaja, J. / Cox-Livingstone, S. / Rossjohn, J. / ...Authors: Moradi, S. / Stankovic, S. / O'Connor, G.M. / Pymm, P. / MacLachlan, B.J. / Faoro, C. / Retiere, C. / Sullivan, L.C. / Saunders, P.M. / Widjaja, J. / Cox-Livingstone, S. / Rossjohn, J. / Brooks, A.G. / Vivian, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pag.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pag.ent.gz | 197.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/6pag ftp://data.pdbj.org/pub/pdb/validation_reports/pa/6pag | HTTPS FTP |
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-Related structure data
Related structure data | 6pa1C 1efxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31874.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10321 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1034.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS |
#4: Protein | Mass: 22386.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL3, CD158B2, KIRCL23, NKAT2 / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43628 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M Ammonium acetate, 0.1 M Tris-HCl pH.8.0 and 25% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 21403 / % possible obs: 98.5 % / Redundancy: 3.1 % / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 2136 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EFX Resolution: 2.501→32.567 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→32.567 Å
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Refine LS restraints |
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LS refinement shell |
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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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