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Yorodumi- PDB-6z9x: Human Class I Major Histocompatibility Complex, A02 allele, prese... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z9x | ||||||
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Title | Human Class I Major Histocompatibility Complex, A02 allele, presenting LLS (t-butyl)Y FGTPT | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC I | ||||||
Function / homology | Function and homology information 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 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 / Endosomal/Vacuolar pathway ...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 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 / Endosomal/Vacuolar pathway / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / 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 / 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 / negative regulation of epithelial cell proliferation / 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 / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å | ||||||
Authors | Rizkallah, P.J. / Man, S. / Redman, J.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J Immunol. / Year: 2021 Title: Synthetic Peptides with Inadvertent Chemical Modifications Can Activate Potentially Autoreactive T Cells. Authors: Man, S. / Redman, J.E. / Cross, D.L. / Cole, D.K. / Can, I. / Davies, B. / Hashimdeen, S.S. / Reid, R. / Llewellyn-Lacey, S. / Miners, K.L. / Ladell, K. / Lissina, A. / Brown, P.E. / ...Authors: Man, S. / Redman, J.E. / Cross, D.L. / Cole, D.K. / Can, I. / Davies, B. / Hashimdeen, S.S. / Reid, R. / Llewellyn-Lacey, S. / Miners, K.L. / Ladell, K. / Lissina, A. / Brown, P.E. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z9x.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z9x.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 6z9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/6z9x ftp://data.pdbj.org/pub/pdb/validation_reports/z9/6z9x | HTTPS FTP |
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-Related structure data
Related structure data | 6z9vC 6z9wC 5eulS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7 #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: 1038.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 4000, 0.1 M Cacodylate buffer, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.68→51.34 Å / Num. obs: 22144 / % possible obs: 81.9 % / Redundancy: 2.5 % / CC1/2: 0.916 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.127 / Rrim(I) all: 0.216 / Net I/σ(I): 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EUL Resolution: 2.68→51.34 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.828 / SU B: 20.185 / SU ML: 0.206 / SU R Cruickshank DPI: 0.0656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.32 Å2 / Biso mean: 21.665 Å2 / Biso min: 3.81 Å2
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Refinement step | Cycle: final / Resolution: 2.68→51.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.685→2.754 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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