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Yorodumi- PDB-1r5w: Evidence that structural rearrangements and/or flexibility during... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r5w | ||||||
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Title | Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T-cell activation | ||||||
Components |
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Keywords | SIGNALING PROTEIN / TCR / MHC class II / structural rearangement | ||||||
Function / homology | Function and homology information peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Krogsgaard, M. / Prado, N. / Adams, E. / He, X. / Chow, D.C. / Wilson, D.B. / Garcia, K.C. / Davis, M.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation Authors: Krogsgaard, M. / Prado, N. / Adams, E.J. / He, X.L. / Chow, D.C. / Wilson, D.B. / Garcia, K.C. / Davis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r5w.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r5w.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r5w_validation.pdf.gz | 391.3 KB | Display | wwPDB validaton report |
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Full document | 1r5w_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 1r5w_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 1r5w_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/1r5w ftp://data.pdbj.org/pub/pdb/validation_reports/r5/1r5w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 20962.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyss / References: UniProt: P04224 #2: Protein | Mass: 21737.195 Da / Num. of mol.: 2 / Mutation: S8C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyss / References: UniProt: Q31164 #3: Protein/peptide | Mass: 1460.715 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: artificial |
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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: 3.28 Å3/Da / Density % sol: 62.49 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 26403 / Num. obs: 26403 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.436 / % possible all: 83.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 82306 |
Reflection shell | *PLUS % possible obs: 83.2 % / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 18.332 Å2 / ksol: 0.288609 e/Å3 | ||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree: 0.487 / Rfactor Rwork: 0.471 | ||||||||||||||||||||
Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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