+Open data
-Basic information
Entry | Database: PDB / ID: 3of6 | ||||||
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Title | Human pre-T cell receptor crystal structure | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig fold | ||||||
Function / homology | Function and homology information negative regulation of thymocyte apoptotic process / NOTCH3 Intracellular Domain Regulates Transcription / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pang, S.S. | ||||||
Citation | Journal: Nature / Year: 2010 Title: The structural basis for autonomous dimerization of the pre-T-cell antigen receptor Authors: Pang, S.S. / Berry, R. / Chen, Z. / Kjer-Nielsen, L. / Perugini, M.A. / King, G.F. / Wang, C. / Chew, S.H. / La Gruta, N.L. / Williams, N.K. / Beddoe, T. / Tiganis, T. / Cowieson, N.P. / ...Authors: Pang, S.S. / Berry, R. / Chen, Z. / Kjer-Nielsen, L. / Perugini, M.A. / King, G.F. / Wang, C. / Chew, S.H. / La Gruta, N.L. / Williams, N.K. / Beddoe, T. / Tiganis, T. / Cowieson, N.P. / Godfrey, D.I. / Purcell, A.W. / Wilce, M.C.J. / 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 | 3of6.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3of6.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 3of6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/3of6 ftp://data.pdbj.org/pub/pdb/validation_reports/of/3of6 | HTTPS FTP |
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-Related structure data
Related structure data | 1kgcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28607.553 Da / Num. of mol.: 3 / Fragment: ectodomain / Mutation: C192A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HiFIVE insect cells / Production host: Trichoplusia ni (cabbage looper) #2: Protein | Mass: 13387.915 Da / Num. of mol.: 3 / Fragment: ectodomain, UNP residues 17-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HiFIVE insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ISU1 #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Sequence details | THE NUMBERING OF THE PROTEIN IS BASED THAT OF A T CELL RECEPTOR AND THERE IS A GAP IN THE NUMBERING ...THE NUMBERING OF THE PROTEIN IS BASED THAT OF A T CELL RECEPTOR AND THERE IS A GAP IN THE NUMBERING IN THE CDR3 LOOP REGION (101-104). FOR CHAINS A,B,C, THE UNICODE IS DEFINE AS P01850. THE N-TERMINAL HALF OF THE PROTEIN (RESIDUE 3-117) IS A VARIABLE REGION OF A T CELL RECEPTOR. THE FIRST FOUR RESIDUES AGSH AND LAST 9 RESIDUES CTSGDDDDK ARE EXPRESSION | |
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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: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M sodium cacodylate, pH 7.0, 0.1M calcium acetate, 13-16% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979461 Å | ||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2009 | ||||||
Radiation | Monochromator: Si Vortex-ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||
Radiation wavelength | Wavelength: 0.979461 Å / Relative weight: 1 | ||||||
Reflection twin | Operator: -k,h+k,l / Fraction: 0.515 | ||||||
Reflection | Resolution: 2.8→67.4 Å / Num. all: 35135 / Num. obs: 35135 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KGC; E chain Resolution: 2.8→67.374 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8277 / σ(F): 1.38 / Phase error: 24.02 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.974 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 244.66 Å2 / Biso mean: 86.0365 Å2 / Biso min: 16.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→67.374 Å
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Refine LS restraints |
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LS refinement shell |
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