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Open data
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Basic information
| Entry | Database: PDB / ID: 2j8u | ||||||
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| Title | Large CDR3a loop alteration as a function of MHC mutation. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / MHC I / MEMBRANE / SECRETED / GLYCATION / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / IMMUNE RESPONSE / DISEASE MUTATION / IMUNOREGULATORY COMPLEX / CLASS I MHC-TCR CO-CRYSTAL | ||||||
| Function / homology | Function and homology informationPhosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / Co-inhibition by PD-1 / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of memory T cell activation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / Co-inhibition by PD-1 / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / Generation of second messenger molecules / tail-anchored membrane protein insertion into ER membrane / Downstream TCR signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / carbohydrate binding / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / immune response / defense response to Gram-positive bacterium / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane Similarity search - Function | ||||||
| Biological species | Homo sapiens (human)![]() HOMO SAPIENS (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Miller, P.J. / Benhar, Y.P. / Biddison, W. / Collins, E.J. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2007Title: Single MHC mutation eliminates enthalpy associated with T cell receptor binding. Authors: Miller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J. | ||||||
| History |
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| Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2j8u.cif.gz | 320.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2j8u.ent.gz | 262.8 KB | Display | PDB format |
| PDBx/mmJSON format | 2j8u.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j8u ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j8u | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 2jccC ![]() 2uweC ![]() 1lp9S C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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Components
| #1: Protein | Mass: 31796.098 Da / Num. of mol.: 2 / Fragment: ECTO-DOMAIN, RESIDUES 25-299 / Mutation: K66A Source method: isolated from a genetically manipulated source Details: MUTATION OF HLA-A2.1 AT POSITION 66 LYSINE TO ALANINE Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HAS EXTRA METHIONINE DUE TO E. COLI EXPRESSION / Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: ![]() #3: Protein/peptide | Mass: 1049.263 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: SELF-PEPTIDE RECOGNIZED BY AHIII T CELL CLONE WHEN PRESENTED BY HLA-A2.1 Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NPA0*PLUS#4: Protein | Mass: 21656.322 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 26890.883 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Compound details | ENGINEERED | Has protein modification | Y | Sequence details | MUTANT K66A ADDITIONAL | |
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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: 2.45 Å3/Da / Density % sol: 29.86 % / Description: NONE |
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| Crystal grow | pH: 6.5 / Details: 1.0 M NACL 20% PEG 8000 MES, PH 6.5 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
| Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2005 / Details: MIRRORS |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.88→30 Å / Num. obs: 38683 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7 |
| Reflection shell | Resolution: 2.88→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.3 / % possible all: 69 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1LP9 Resolution: 2.88→122.17 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / SU B: 52.965 / SU ML: 0.46 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES IN THE TCR ALPHA CHAINS E AND L 50- 59 ARE COMPLETELY DISORDERED IN THE STRUCTURE AND THUS THE COORDINATES HAVE AN OCCUPANCY OF 0.0
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 46.64 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.88→122.17 Å
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About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
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