+Open data
-Basic information
Entry | Database: PDB / ID: 5w69 | ||||||
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Title | HLA-C*06:02 presenting ARFNDLRFV | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / Antigen presentation / Human Leukocyte Antigen | ||||||
Function / homology | Function and homology information peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / RUNX3 regulates WNT signaling / negative regulation of CD4-positive, alpha-beta T cell differentiation / response to transforming growth factor beta / RUNX3 regulates YAP1-mediated transcription ...peripheral nervous system neuron development / RUNX3 regulates RUNX1-mediated transcription / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates BCL2L11 (BIM) transcription / RUNX3 regulates WNT signaling / negative regulation of CD4-positive, alpha-beta T cell differentiation / response to transforming growth factor beta / RUNX3 regulates YAP1-mediated transcription / chromatin => GO:0000785 / RUNX3 Regulates Immune Response and Cell Migration / RUNX3 regulates NOTCH signaling / RUNX3 regulates CDKN1A transcription / regulation of cell differentiation / RUNX3 regulates p14-ARF / hemopoiesis / negative regulation of cell cycle / TAP binding / chondrocyte differentiation / ossification / 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 / DAP12 interactions / negative regulation of receptor 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 ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of RUNX3 expression and activity / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / neuron differentiation / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / positive regulation of cellular senescence / peptide antigen binding / 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 / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / protein phosphorylation / intracellular membrane-bounded organelle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mobbs, J.I. / Vivian, J.P. / Rossjohn, J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. Authors: Mobbs, J.I. / Illing, P.T. / Dudek, N.L. / Brooks, A.G. / Baker, D.G. / Purcell, A.W. / Rossjohn, J. / 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 | 5w69.cif.gz | 645.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w69.ent.gz | 532.8 KB | Display | PDB format |
PDBx/mmJSON format | 5w69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w69_validation.pdf.gz | 477.4 KB | Display | wwPDB validaton report |
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Full document | 5w69_full_validation.pdf.gz | 484.4 KB | Display | |
Data in XML | 5w69_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 5w69_validation.cif.gz | 86.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w69 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w69 | HTTPS FTP |
-Related structure data
Related structure data | 5w67C 5w6aC 4nt6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 32087.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q29963, UniProt: P10321*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1139.307 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q13761*PLUS #4: Water | ChemComp-HOH / | |
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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: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M Na acetate and 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→74.34 Å / Num. obs: 52631 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 51.22 Å2 / Rpim(I) all: 0.11 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.8→2.89 Å / Redundancy: 9.2 % / Num. unique obs: 4512 / Rpim(I) all: 0.51 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NT6 Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.317
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Displacement parameters | Biso mean: 34.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→40.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / 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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