+Open data
-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 information Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / PD-1 signaling / 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 / T cell mediated cytotoxicity directed against tumor cell target ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / EMC complex / PD-1 signaling / 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 / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / 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 / 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 / response to bacterium / 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 / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / carbohydrate binding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) MUS MUSCULUS (house mouse) 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: 2007 Title: 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j8u.cif.gz | 320.2 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 (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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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: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS #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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIP / References: UniProt: P61769 #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.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII 12.2 T CELL CLONE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P01849*PLUS #5: Protein | Mass: 26890.883 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: B6 / Cell: T CELL / Cell line: AHIII 12.2 T CELL CLONE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: P04213*PLUS Compound details | ENGINEERED | 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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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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Refine LS restraints |
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