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Yorodumi- PDB-2axh: Crystal structures of T cell receptor beta chains related to rheu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2axh | ||||||
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Title | Crystal structures of T cell receptor beta chains related to rheumatoid arthritis | ||||||
Components | T cell receptor beta chain | ||||||
Keywords | IMMUNE SYSTEM / TCR | ||||||
Function / homology | Function and homology information alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Li, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis. Authors: Li, H. / Van Vranken, S. / Zhao, Y. / Li, Z. / Guo, Y. / Eisele, L. / Li, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2axh.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2axh.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 2axh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2axh_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 2axh_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 2axh_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 2axh_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/2axh ftp://data.pdbj.org/pub/pdb/validation_reports/ax/2axh | HTTPS FTP |
-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27607.275 Da / Num. of mol.: 2 / Fragment: extracellular domain / Mutation: F104Y, C187S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01850 #2: Water | ChemComp-HOH / | |
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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: 3.95 Å3/Da / Density % sol: 69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.6-0.7m sodium citrate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.7→39.2 Å / Num. all: 24987 / Num. obs: 24387 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 79.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 35 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.478 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→39.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2028564.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2572 Å2 / ksol: 0.359192 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→39.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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