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- PDB-2p5e: Crystal Structures of High Affinity Human T-Cell Receptors Bound ... -

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Basic information

Entry
Database: PDB / ID: 2p5e
TitleCrystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry
Components
  • Beta-2-microglobulin
  • Cancer/testis antigen 1B
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Hypothetical protein
  • T-Cell Receptor, Alpha Chain
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR / CDR3 / PHAGE DISPLAY / MUTANT / HIGH AFFINITY / NY-ESO-1
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 / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...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 / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / antibacterial humoral response / positive regulation of protein binding / MHC class II protein complex binding / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...CTAG/Pcc1 family / Transcription factor Pcc1 / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 subtype 2 / Immunoglobulin C-2 Type / 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 subtype / Immunoglobulin / 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
ISOPROPYL ALCOHOL / V-alpha FR1 / T cell receptor alpha chain constant / 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: 1.89 Å
AuthorsSami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. ...Sami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2007
Title: Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry
Authors: Sami, M. / Rizkallah, P.J. / Dunn, S. / Molloy, P. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Yi, L. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Sequence No suitable database reference was found for Chains D and E at time of processing

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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, A-2 alpha chain
B: Beta-2-microglobulin
C: Cancer/testis antigen 1B
D: T-Cell Receptor, Alpha Chain
E: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,06421
Polymers93,5245
Non-polymers1,54016
Water13,313739
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-134 kcal/mol
Surface area36830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.002, 51.771, 118.270
Angle α, β, γ (deg.)90.00, 98.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA2 AND ALPHA3, RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PEX078 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11853.319 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) / Gene: B2M / Plasmid: PEX050 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein T-Cell Receptor, Alpha Chain


Mass: 21406.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A2NVQ1, UniProt: P01848*PLUS
#5: Protein Hypothetical protein


Mass: 27218.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q2YDB4

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cancer/testis antigen 1B / L antigen family member 2 / LAGE-2 protein / Autoimmunogenic cancer/testis antigen NY-ESO-1


Mass: 1094.347 Da / Num. of mol.: 1 / Fragment: RESIDUES 157-165 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMANS)
References: UniProt: P78358

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Non-polymers , 6 types, 755 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2005 / Details: MIRROR + MONOCHROMATOR
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.887→117 Å / Num. obs: 69966

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F53

2f53


Resolution: 1.89→117.04 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.074 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23579 3552 5.1 %RANDOM
Rwork0.17777 ---
obs0.18071 66411 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.457 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å21.52 Å2
2--0.3 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.89→117.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 93 739 7400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216915
X-RAY DIFFRACTIONr_bond_other_d0.0030.024691
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9449412
X-RAY DIFFRACTIONr_angle_other_deg0.713.00311347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8175837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.27323.83342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.812151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5581548
X-RAY DIFFRACTIONr_chiral_restr0.0880.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021449
X-RAY DIFFRACTIONr_nbd_refined0.1960.31430
X-RAY DIFFRACTIONr_nbd_other0.2130.35260
X-RAY DIFFRACTIONr_nbtor_refined0.1870.53220
X-RAY DIFFRACTIONr_nbtor_other0.0920.53598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.5979
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1910.54
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.344
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.3104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.545
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.07225262
X-RAY DIFFRACTIONr_mcbond_other0.8621659
X-RAY DIFFRACTIONr_mcangle_it3.54436703
X-RAY DIFFRACTIONr_scbond_it5.40943290
X-RAY DIFFRACTIONr_scangle_it7.09162703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.887→1.936 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 240 -
Rwork0.256 4475 -
obs--89.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2966-0.0416-0.8640.7292-0.19311.8137-0.0310.0066-0.06590.0236-0.0140.0090.08550.11860.045-0.08480.02840.0111-0.1070.0065-0.080215.8288-2.512140.6213
20.92470.16510.190.9099-1.01482.87260.0554-0.2726-0.00830.1119-0.0216-0.0779-0.1640.3882-0.0338-0.0297-0.0175-0.01720.1095-0.0323-0.035811.8696-10.095275.6826
32.0280.6101-1.27532.4276-0.66951.9772-0.0141-0.0233-0.1015-0.1223-0.05840.01790.2579-0.02970.0724-0.05010.0008-0.0046-0.1087-0.0071-0.08014.4083-20.224556.911
41.065-0.4988-1.12293.6430.16961.2212-0.0148-0.0978-0.21180.1790.00330.3012-0.10060.23720.0115-0.02310.0345-0.0029-0.0269-0.0066-0.060917.70360.555632.5599
51.98970.7825-1.45331.196-0.64973.14890.02550.12860.17860.0039-0.0131-0.0519-0.3630.1004-0.0124-0.0337-0.0146-0.0292-0.02070.0417-0.026523.016215.512415.1694
61.87290.6469-0.30273.7244-0.50662.9899-0.10240.19560.147-0.16780.11950.3156-0.4396-0.0375-0.01710.0104-0.0682-0.01560.1010.0569-0.019523.233517.3856-19.8545
70.5465-0.18750.67060.8074-0.1772.0724-0.00310.0912-0.0556-0.0384-0.0270.0060.1601-0.01350.0301-0.12690.0091-0.0218-0.0293-0.019-0.09078.0433-0.725511.2251
81.81860.54520.13850.8446-0.20971.4263-0.01230.11140.0023-0.06830.002-0.0186-0.06920.18650.0103-0.0746-0.0285-0.0117-0.0179-0.0098-0.09219.40652.9472-17.4513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION2AA185 - 274185 - 274
3X-RAY DIFFRACTION3BB0 - 991 - 100
4X-RAY DIFFRACTION4CC1 - 91 - 9
5X-RAY DIFFRACTION5DD1 - 1102 - 111
6X-RAY DIFFRACTION6DD115 - 191116 - 192
7X-RAY DIFFRACTION7EE1 - 1101 - 110
8X-RAY DIFFRACTION8EE120 - 241120 - 241

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