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Open data
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Basic information
| Entry | Database: PDB / ID: 9d97 | ||||||
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| Title | KIR3DL1 - HLA-B*38-YHE complex | ||||||
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Keywords | IMMUNE SYSTEM / Killer Immunoglobulin-like receptor / Human Leucocyte Antigen / immune complex / NK cell | ||||||
| Function / homology | Function and homology informationHLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / : / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / : / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / natural killer cell mediated cytotoxicity / cellular response to insulin-like growth factor stimulus / cyclin A2-CDK2 complex / G2 Phase / p53-Dependent G1 DNA Damage Response / antigen processing and presentation of peptide antigen via MHC class I / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / regulation of DNA replication / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / cellular response to platelet-derived growth factor stimulus / cellular response to nitric oxide / post-translational protein modification / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / cellular response to iron(III) ion / cellular response to estradiol stimulus / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / G1/S transition of mitotic cell cycle / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Orc1 removal from chromatin / positive regulation of fibroblast proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / Regulation of TP53 Degradation / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / Processing of DNA double-strand break ends / protein refolding / Senescence-Associated Secretory Phenotype (SASP) / early endosome membrane / protein homotetramerization / cellular response to hypoxia Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Zhu, S. / Vivian, J. / Petersen, J. / Rossjohn, J. | ||||||
| Funding support | Australia, 1items
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Citation | Journal: To Be PublishedTitle: The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis Authors: Ladell, K. / Zhu, S. / Kaufmann, M. / Vivian, J. / Petersen, J. / Rossjohn, J. / Price, D. / Fugger, L. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9d97.cif.gz | 355.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9d97.ent.gz | 236.2 KB | Display | PDB format |
| PDBx/mmJSON format | 9d97.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9d97_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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| Full document | 9d97_full_validation.pdf.gz | 474.8 KB | Display | |
| Data in XML | 9d97_validation.xml.gz | 36.8 KB | Display | |
| Data in CIF | 9d97_validation.cif.gz | 51.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/9d97 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/9d97 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9d95C ![]() 9d96C C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| Unit cell |
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Components
-Protein , 3 types, 3 molecules ABG
| #1: Protein | Mass: 32029.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-DRB1 / Production host: ![]() |
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| #2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: ![]() |
| #4: Protein | Mass: 33220.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Production host: Homo sapiens (human) / References: UniProt: P43629 |
-Protein/peptide / Sugars / Non-polymers , 3 types, 575 molecules C



| #3: Protein/peptide | Mass: 1192.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: synthetic construct (others) / References: UniProt: P20248 | ||
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| #5: Sugar | | #6: Water | ChemComp-HOH / | |
-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.16 % |
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| Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 15% PEG 3350, 2% Tacsimate, pH 5.0, 0.1 M Na3citrate, pH 5.6 |
-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: 95368 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2021 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 95368 Å / Relative weight: 1 |
| Reflection | Resolution: 1.6→44.74 Å / Num. obs: 84176 / % possible obs: 96.16 % / Redundancy: 4.1 % / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.05153 / Net I/σ(I): 8.61 |
| Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 8259 / CC1/2: 0.531 / CC star: 0.833 / Rpim(I) all: 0.4862 / % possible all: 95.49 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.74 Å / SU ML: 0.163 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.7776 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 29.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.6→44.74 Å
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
Australia, 1items
Citation



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