+Open data
-Basic information
Entry | Database: PDB / ID: 3tf7 | ||||||
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Title | 42F3 QL9/H2-Ld complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig and MHC / Antigen Recognition / TCR-pMHC / Membrane Receptors | ||||||
Function / homology | Function and homology information oxoglutarate dehydrogenase (NAD+) activity / Lysine catabolism / olfactory bulb mitral cell layer development / Citric acid cycle (TCA cycle) / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation ...oxoglutarate dehydrogenase (NAD+) activity / Lysine catabolism / olfactory bulb mitral cell layer development / Citric acid cycle (TCA cycle) / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / pyramidal neuron development / thalamus development / 2-oxoglutarate metabolic process / striatum development / NADH metabolic process / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / thiamine pyrophosphate binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / tricarboxylic acid cycle / heat shock protein binding / T cell receptor binding / generation of precursor metabolites and energy / lumenal side of endoplasmic reticulum membrane / hippocampus development / mitochondrial membrane / glycolytic process / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / mitochondrion / extracellular space / metal ion binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Adams, J.J. / Kranz, D.M. / Garcia, K.C. | ||||||
Citation | Journal: Immunity / Year: 2011 Title: T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Authors: Adams, J.J. / Narayanan, S. / Liu, B. / Birnbaum, M.E. / Kruse, A.C. / Bowerman, N.A. / Chen, W. / Levin, A.M. / Connolly, J.M. / Zhu, C. / Kranz, D.M. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tf7.cif.gz | 516.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tf7.ent.gz | 431.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/3tf7 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tf7 | HTTPS FTP |
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-Related structure data
Related structure data | 3tfkC 3tjhC 3tpuC 2oi9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21072.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS #2: Protein/peptide | Mass: 1063.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Anaspec / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60597*PLUS #3: Protein | Mass: 27494.252 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #4: Chemical | Sequence details | THE 42F3 PROTEIN (CHAIN C,G I AND K) IS A SINGLE CHAIN FV FRAGMENT OF THE THE 42F3 ALPHA BETA TCR. ...THE 42F3 PROTEIN (CHAIN C,G I AND K) IS A SINGLE CHAIN FV FRAGMENT OF THE THE 42F3 ALPHA BETA TCR. THE FV FRAGMENT IS DERIVED FROM TWO PROTEIN CHAINS (ALPHA AND BETA) AND FUSED TOGETHER WITH AN UNNATURAL LINKER SEQUENCE (GGGGSGGGGS | |
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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: 3.9 Å3/Da / Density % sol: 68.42 % |
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Crystal grow | Temperature: 298 K / pH: 8.25 Details: 7% (w/v) PEG 17500, 100mM Bicine pH 8.25. 30% Glycerol cryo addiditive, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 61762 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 2.75→2.85 Å / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OI9 Resolution: 2.75→37.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 27.259 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→37.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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