+Open data
-Basic information
Entry | Database: PDB / ID: 7s7e | ||||||
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Title | STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PEPTIDE | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / DOT1L PEPTIDE / MHC-I / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / CANCER | ||||||
Function / homology | Function and homology information histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / regulation of interleukin-6 production ...histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / regulation of interleukin-6 production / histone methyltransferase activity / TAP binding / protection from natural killer cell mediated cytotoxicity / heterochromatin formation / detection of bacterium / telomere organization / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / DNA damage checkpoint signaling / 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 / 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 / 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 / PKMTs methylate histone lysines / MHC class I protein complex / defense response / 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 / 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 / gene expression / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / methylation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / RNA polymerase II-specific DNA-binding transcription factor binding / amyloid fibril formation / nucleic acid binding / transcription coactivator activity / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / intracellular membrane-bounded organelle / DNA repair / innate immune response / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / 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 | 7s7e.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s7e.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 7s7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s7e_validation.pdf.gz | 750 KB | Display | wwPDB validaton report |
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Full document | 7s7e_full_validation.pdf.gz | 752.7 KB | Display | |
Data in XML | 7s7e_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 7s7e_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/7s7e ftp://data.pdbj.org/pub/pdb/validation_reports/s7/7s7e | HTTPS FTP |
-Related structure data
Related structure data | 7rzdSC 7rzjC 7s79C 7s7dC 7s7fC 7s8aC 7s8eC 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
-Protein , 2 types, 2 molecules AB
#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: PET30a / 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: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
-Protein/peptide / Sugars , 2 types, 2 molecules C
#3: Protein/peptide | Mass: 934.069 Da / Num. of mol.: 1 / Fragment: DOT1L(998-1006) PEPTIDE / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q8TEK3, [histone H3]-lysine79 N-trimethyltransferase |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose |
-Non-polymers , 2 types, 409 molecules
#5: Chemical | ChemComp-NA / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.83 Å3/Da / Density % sol: 56.59 % / 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2020 / Details: Si(111) MONOCHROMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→29.22 Å / Num. obs: 34270 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2435 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RZD Resolution: 2.04→29.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.997 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.162 / 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: 115.62 Å2 / Biso mean: 35.045 Å2 / Biso min: 15.78 Å2
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Refinement step | Cycle: final / Resolution: 2.04→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.093 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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