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

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Basic information

Entry
Database: PDB / ID: 2bnq
TitleStructural and kinetic basis for heightened immunogenicity of T cell vaccines
Components
  • (T-CELL RECEPTOR ...) x 2
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
  • SYNTHETIC PEPTIDEPeptide synthesis
KeywordsIMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR-COMPLEX / TCR / MHC / IMMUNODOMINANCE / FLU / COMPLEX / TRANSMEMBRANE / GLYCOPROTEIN / POLYMORPHISM / T-CELL / RECEPTOR / SUPERAGONIST PEPTIDE T-CELL VACCINES / IMMUNE SYSTEM-RECEPTOR complex
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin ...CTAG/Pcc1 family / Transcription factor Pcc1 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21 / T cell receptor beta variable 6-5 / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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. / Boultier, 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. / Boultier, J.M. / Rizkallah, P. / Renner, C. / Sewell, A. / Van Der Merwe, P.A. / Jackobsen, 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
DepositionMar 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references / Derived calculations ...Database references / 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: SYNTHETIC PEPTIDE
D: T-CELL RECEPTOR ALPHA CHAIN V REGION
E: T-CELL RECEPTOR BETA CHAIN C REGION


Theoretical massNumber of molelcules
Total (without water)94,0985
Polymers94,0985
Non-polymers00
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-61.6 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.563, 62.490, 116.955
Angle α, β, γ (deg.)90.00, 105.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / MHC / A-2 ALPHA CHAIN PRECURSOR


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1, -2, -3, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: REFOLDED FROM INCLUSION BODIES / Cell: ANTIGEN PRESENTING CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin / HDCMA22P / B2M


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: BETA-2-MICROGLOBULIN, RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: REFOLDED FROM INCLUSION BODIES FROM INCLUSION BODIES
Cell: ANTIGEN PRESENTING CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P61769

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T-CELL RECEPTOR ... , 2 types, 2 molecules DE

#4: Protein T-CELL RECEPTOR ALPHA CHAIN V REGION


Mass: 22171.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS ALSO C (CONSTANT) REGION / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYTEM / Description: REFOLDED FROM INCLUSION BODIES / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: A0A0B4J279*PLUS
#5: Protein T-CELL RECEPTOR BETA CHAIN C REGION / TRBC1


Mass: 27005.988 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: IMMUNE SYTEM / Description: REFOLDED FROM INCLUSION BODIES. / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01850, UniProt: A0A0K0K1A5*PLUS

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Protein/peptide / Non-polymers , 2 types, 528 molecules C

#3: Protein/peptide SYNTHETIC PEPTIDE / Peptide synthesis


Mass: 1090.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: REFOLDED FROM INCLUSION BODIES. PEPTIDE CHAIN C. / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P78358*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growpH: 7.2 / Details: pH 7.20

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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: 1.7→20 Å / Num. obs: 112638 / % possible obs: 89.3 % / Observed criterion σ(I): 0.9 / Redundancy: 8 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.4
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 58

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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: 1.7→19.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 217685.72 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4779 5.1 %RANDOM
Rwork0.226 ---
obs0.226 94142 84.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6969 Å2 / ksol: 0.358549 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.93 Å20 Å2-1.66 Å2
2--12.31 Å20 Å2
3----6.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 0 527 7153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 237 5 %
Rwork0.307 4469 -
obs--42.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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