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Yorodumi- PDB-4mnq: TCR-peptide specificity overrides affinity enhancing TCR-MHC inte... -
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-Basic information
Entry | Database: PDB / ID: 4mnq | ||||||
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Title | TCR-peptide specificity overrides affinity enhancing TCR-MHC interactions | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Surface plasmon resonance (SPR) / BIAcoreTM / peptide-major histocompatibility complex (pMHC): T-cell receptor (TCR) / T-cells / high affinity TCR / two-step binding / adoptive therapy / Immunoglobulin / Adaptive immune response | ||||||
Function / homology | Function and homology information positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / telomerase activity ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / : / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / nuclear telomere cap complex / siRNA processing / alpha-beta T cell receptor complex / Telomere Extension By Telomerase / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / T cell receptor complex / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of G1/S transition of mitotic cell cycle / telomeric DNA binding / DNA biosynthetic process / RNA-templated transcription / CD8 receptor binding / positive regulation of stem cell proliferation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / mitochondrial nucleoid / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of cellular senescence / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / Generation of second messenger molecules / telomere maintenance via telomerase / protection from natural killer cell mediated cytotoxicity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of Wnt signaling pathway / replicative senescence / PD-1 signaling / beta-2-microglobulin binding / negative regulation of endothelial cell apoptotic process / T cell receptor binding / response to cadmium ion / detection of bacterium / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of miRNA transcription / positive regulation of receptor binding / early endosome lumen / mitochondrion organization / Nef mediated downregulation of MHC class I complex cell surface expression / positive regulation of nitric-oxide synthase activity / negative regulation of receptor binding / DAP12 interactions / 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 glucose import / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Formation of the beta-catenin:TCF transactivating complex / 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 / regulation of protein stability / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / PML body / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / RNA-directed DNA polymerase Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Pan troglodytes (chimpanzee) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.742 Å | ||||||
Authors | Rizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Jakobsen, B.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions. Authors: Cole, D.K. / Miles, K.M. / Madura, F. / Holland, C.J. / Schauenburg, A.J. / Godkin, A.J. / Bulek, A.M. / Fuller, A. / Akpovwa, H.J. / Pymm, P.G. / Liddy, N. / Sami, M. / Li, Y. / Rizkallah, ...Authors: Cole, D.K. / Miles, K.M. / Madura, F. / Holland, C.J. / Schauenburg, A.J. / Godkin, A.J. / Bulek, A.M. / Fuller, A. / Akpovwa, H.J. / Pymm, P.G. / Liddy, N. / Sami, M. / Li, Y. / Rizkallah, P.J. / Jakobsen, B.K. / Sewell, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mnq.cif.gz | 346.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mnq.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mnq_validation.pdf.gz | 488.2 KB | Display | wwPDB validaton report |
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Full document | 4mnq_full_validation.pdf.gz | 511.1 KB | Display | |
Data in XML | 4mnq_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 4mnq_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/4mnq ftp://data.pdbj.org/pub/pdb/validation_reports/mn/4mnq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P61769 |
#4: Protein | Mass: 22245.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pan troglodytes (chimpanzee), (gene. exp.) Homo sapiens (human) Gene: LOC452776 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: H2RG00, UniProt: K7N5M9 |
#5: Protein | Mass: 27135.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV13S1, TRBC1 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: A0A585, UniProt: P01850 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1142.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MAGE hTERT 540-548 sequence / Source: (synth.) Homo sapiens (human) / References: UniProt: O14746, RNA-directed DNA polymerase |
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-Non-polymers , 3 types, 24 molecules
#6: Chemical | ChemComp-GOL / | ||
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#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: TRIS 0.02M, 20% PEG 4000, 0.01M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012 | ||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.74→42.15 Å / Num. obs: 26577 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.3 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.742→42.15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 37.958 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.742→42.15 Å
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