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Yorodumi- PDB-7s8e: STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s8e | ||||||
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Title | STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE AND BOUND GLYCEROL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MLL PEPTIDE / MHC-I / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / NEOANTIGEN / CANCER | ||||||
Function / homology | Function and homology information protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / embryonic hemopoiesis / anterior/posterior pattern specification / exploration behavior / histone methyltransferase complex / : / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / TAP binding / protection from natural killer cell mediated cytotoxicity / spleen development / transcription initiation-coupled chromatin remodeling / 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 transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / detection of bacterium / post-embryonic development / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / visual learning / 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 / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / PKMTs methylate histone lysines / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / Transcriptional regulation of granulopoiesis / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of protein binding / ER-Phagosome pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Patskovsky, Y. / Nyovanie, S. / Patskovska, L. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovsky, Y. / Nyovanie, S. / Patskovska, L. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R. / Findeis, M. / Hurwitz, A. / Van Dijk, M. / Buell, J. / Underwood, D. / Krogsgaard, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular mechanism of phosphopeptide neoantigen immunogenicity. Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. ...Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. / Hurwitz, A. / Van Dijk, M. / Chantzoura, E. / Yague, A.S. / Pollack Smith, D. / Buell, J.S. / Underwood, D. / Krogsgaard, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s8e.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s8e.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 7s8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/7s8e ftp://data.pdbj.org/pub/pdb/validation_reports/s8/7s8e | HTTPS FTP |
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-Related structure data
Related structure data | 7rzdC 7rzjSC 7s79C 7s7dC 7s7eC 7s7fC 7s8aC 7s8fC 7s8iC 7s8jC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31962.016 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889 | ||||
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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 / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1109.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03164 | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.53 % / Description: RODS |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 13, 2018 / Details: SI 111 CRYSTAL |
Radiation | Monochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.54 Å / Num. obs: 69841 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3393 / CC1/2: 0.55 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RZJ Resolution: 1.6→45.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.652 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.38 Å2 / Biso mean: 24.974 Å2 / Biso min: 11.16 Å2
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Refinement step | Cycle: final / Resolution: 1.6→45.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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