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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-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
  • SYNTHETIC PEPTIDE
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 / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / alpha-beta T cell activation / beta-2-microglobulin binding / Generation of second messenger molecules / endoplasmic reticulum exit site / Co-inhibition by PD-1 / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / external side of plasma membrane / innate immune response
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 / 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


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


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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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