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- PDB-2bnu: Structural and kinetic basis for heightened immunogenicity of T c... -

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Basic information

Entry
Database: PDB / ID: 2bnu
TitleStructural and kinetic basis for heightened immunogenicity of T cell vaccines
Components
  • T-CELL RECEPTOR ALPHA CHAIN C REGION
  • T-CELL RECEPTOR BETA CHAIN C REGION
KeywordsIMMUNE 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
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21 / T cell receptor beta variable 6-5 / T cell receptor alpha chain constant / T cell receptor beta constant 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, 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
DepositionApr 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-CELL RECEPTOR ALPHA CHAIN C REGION
B: T-CELL RECEPTOR BETA CHAIN C REGION


Theoretical massNumber of molelcules
Total (without water)49,2202
Polymers49,2202
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-31.3 kcal/mol
Surface area24420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)42.991, 60.295, 82.641
Angle α, β, γ (deg.)90.00, 89.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-CELL RECEPTOR ALPHA CHAIN C REGION / TCR ALPHA CHAIN


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 T-CELL RECEPTOR BETA CHAIN C REGION / TCR BETA CHAIN


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 39.96 %
Crystal growpH: 6.8 / Details: PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.4→1.46 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 62.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGA

1oga


Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 /
RfactorNum. reflection
Rwork0.245 -
obs0.245 85029
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 0 243 3705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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