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Yorodumi- PDB-3kxf: Crystal Structure of SB27 TCR in complex with the 'restriction tr... -
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-Basic information
Entry | Database: PDB / ID: 3kxf | ||||||
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Title | Crystal Structure of SB27 TCR in complex with the 'restriction triad' mutant HLA-B*3508-13mer | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / HLA / TCR / Disulfide bond / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / alpha-beta T cell activation / TAP binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / detection of bacterium / 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 / 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 / defense response / 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 / 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 / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / sequence-specific DNA binding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / protein dimerization activity / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Archbold, J.K. / Tynan, F.E. / Gras, S. / Rossjohn, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / ...Authors: Burrows, S.R. / Chen, Z. / Archbold, J.K. / Tynan, F.E. / Beddoe, T. / Kjer-Nielsen, L. / Miles, J.J. / Khanna, R. / Moss, D.J. / Liu, Y.C. / Gras, S. / Kostenko, L. / Brennan, R.M. / Clements, C.S. / Brooks, A.G. / Purcell, A.W. / McCluskey, J. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kxf.cif.gz | 649 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kxf.ent.gz | 546.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kxf_validation.pdf.gz | 546.9 KB | Display | wwPDB validaton report |
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Full document | 3kxf_full_validation.pdf.gz | 598.2 KB | Display | |
Data in XML | 3kxf_validation.xml.gz | 110.6 KB | Display | |
Data in CIF | 3kxf_validation.cif.gz | 150.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kxf ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kxf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 8 molecules ACKIBFLJ
#1: Protein | Mass: 31840.152 Da / Num. of mol.: 4 / Fragment: residues in UNP 25-300 / Mutation: Q65A, T69A, Q155A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS #2: Protein | Mass: 11748.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
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-SB27 T cell receptor ... , 2 types, 8 molecules DGNMEHPO
#3: Protein | Mass: 23251.533 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS #4: Protein | Mass: 27190.182 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A5B9*PLUS |
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-Protein/peptide , 1 types, 4 molecules QRTS
#5: Protein/peptide | Mass: 1426.612 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: synthetic peptide of naturally occurring viral peptide References: UniProt: P03206 |
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-Non-polymers , 2 types, 65 molecules
#6: Chemical | ChemComp-IOD / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE 156TH IN CHAIN A,C,K,I IS VARIANT, B*3508. THE SEQUENCE DATABASE REFERENCE FOR CHAIN D,G,N,M ...THE 156TH IN CHAIN A,C,K,I IS VARIANT, B*3508. THE SEQUENCE DATABASE REFERENCE FOR CHAIN D,G,N,M AND CHAIN E,H,P,O DO NOT CURRENTLY EXIST. |
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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: 2.64 Å3/Da / Density % sol: 53.33 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.7 Details: 0.1M cacodlyate, 0.2M potassium iodide, 18% polyethylene glycol 3350, pH 6.7, vapor diffusion, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 |
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Detector | Date: Mar 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.1→80 Å / Num. obs: 71533 / Redundancy: 5.1 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 3.1→3.2 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→80 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.785 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 52.171 / SU ML: 0.463 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.582 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The file contains friedel pairs.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.8 Å2 / Biso mean: 24.944 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→80 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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