[English] 日本語
Yorodumi- PDB-2bnu: Structural and kinetic basis for heightened immunogenicity of T c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bnu | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and kinetic basis for heightened immunogenicity of T cell vaccines | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/RECEPTOR / SUPERAGONIST PEPTIDE T-CELL VACCINES / RECEPTOR / T-CELL / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / IMMUNE SYSTEM-RECEPTOR complex | ||||||
Function / homology | Function and homology information alpha-beta T cell receptor complex / 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 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling ...alpha-beta T cell receptor complex / 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 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / cell surface receptor signaling pathway / immune response / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. ...Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boultier, J.M. / Rizkallah, P.J. / Renner, C. / Sewell, A. / Van Der Merwe, P.A. / Jackobsen, B.K. / Griffiths, G. / Jones, E.Y. / Cerundolo, V. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2005 Title: Structural and Kinetic Basis for Heightened Immunogenicity of T Cell Vaccines. Authors: Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boulter, J.M. / Rizkallah, P. / Renner, C. / ...Authors: Chen, J.-L. / Stewart-Jones, G. / Bossi, G. / Lissin, N.M. / Wooldridge, L. / Choi, E.M.L. / Held, G. / Dunbar, P.R. / Esnouf, R.M. / Sami, M. / Boulter, J.M. / Rizkallah, P. / Renner, C. / Sewell, A. / Van Der Merwe, P.A. / Jakobsen, B.K. / Griffiths, G. / Jones, E.Y. / Cerundolo, V. #1: Journal: J.Immunol. / Year: 2000 Title: Identification of NY-Eso-1 Peptide Analogues Capable of Improved Stimulation of Tumor-Reactive Ctl Authors: Chen, J.-L. / Dunbar, P.R. / Gileadi, U. / Jager, E. / Gnjatic, S. / Nagata, Y. / Stockert, E. / Panicali, D.L. / Chen, Y.-T. / Knuth, A. / Old, L.J. / Cerundolo, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bnu.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bnu.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bnu_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2bnu_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 2bnu_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 2bnu_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bnu ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bnu | HTTPS FTP |
-Related structure data
Related structure data | 2bnqC 2bnrC 1ogaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22213.588 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-91 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYSTEM / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01848, UniProt: A0A0B4J279*PLUS |
---|---|
#2: Protein | Mass: 27005.988 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYSTEM / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P01848, UniProt: P01850, UniProt: A0A0K0K1A5*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.96 % |
---|---|
Crystal grow | pH: 6.8 / Details: PH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 85029 / % possible obs: 93 % / Observed criterion σ(I): 0.9 / Redundancy: 8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.4→1.46 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 62.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OGA Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|