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- PDB-4jfe: Preservation of peptide specificity during TCR-MHC contact domina... -

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Basic information

Entry
Database: PDB / ID: 4jfe
TitlePreservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR
Components
  • (High Affinity TCR ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma peptide L7A
KeywordsIMMUNE SYSTEM / HLA / TCR / Melanoma / High Affinity
Function / homology
Function and homology information


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 / Golgi medial cisterna / 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 / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse ...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 / Golgi medial cisterna / 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 / 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 / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / antibacterial humoral response / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane
Similarity search - Function
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 / Beta-2-Microglobulin ...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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 chain constant / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Madura, F. / Sewell, A.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: T-cell receptor specificity maintained by altered thermodynamics.
Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / ...Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / Jakobsen, B.K. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Melanoma peptide L7A
D: High Affinity TCR Alpha Chain
E: High Affinity TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75211
Polymers94,1845
Non-polymers5686
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-117 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.610, 121.610, 82.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Melanoma peptide L7A


Mass: 943.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Heteroclitic L7A variant of Melanoma epitope

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High Affinity TCR ... , 2 types, 2 molecules DE

#4: Protein High Affinity TCR Alpha Chain


Mass: 21887.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01848*PLUS
#5: Protein High Affinity TCR Beta Chain


Mass: 27522.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01850*PLUS

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Non-polymers , 3 types, 72 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M BIS TRIS Propane, 20% PEG 4000, 0.2M Ammonium sulphate, 17.4% glycerol, pH 7.0, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorDetector: CCD / Date: Oct 8, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.63→68.13 Å / Num. all: 35640 / Num. obs: 35640 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rsym value: 0.103 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.63-2.78.40.8810.82213626460.881100
2.7-2.788.40.72612125725440.726100
2.78-2.868.40.5791.22071224670.579100
2.86-2.948.30.4561.52028324310.456100
2.94-3.048.30.3372.11954523440.337100
3.04-3.158.30.2552.71869622520.255100
3.15-3.278.30.193.71811921960.19100
3.27-3.48.10.1415.11723421170.141100
3.4-3.558.10.1235.81628920090.123100
3.55-3.7280.0977.21547919360.097100
3.72-3.928.10.0818.31493318550.081100
3.92-4.168.10.0759.21411317420.075100
4.16-4.4580.065101309316290.065100
4.45-4.8180.0678.91228515330.067100
4.81-5.277.90.06110.51120114110.061100
5.27-5.897.90.062101015412830.062100
5.89-6.88.10.06210.3921611380.062100
6.8-8.337.70.04613.874299600.046100
8.33-11.776.80.04115.750797420.04198.8
11.77-54.3455.70.0421523254050.04294.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.64 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å68.13 Å
Translation2.7 Å68.13 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→68.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8484 / SU B: 22.405 / SU ML: 0.222 / SU R Cruickshank DPI: 0.7005 / SU Rfree: 0.3191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.7 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1674 5.1 %RANDOM
Rwork0.202 ---
obs0.2044 32992 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 283.61 Å2 / Biso mean: 62.9147 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→68.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 32 66 6734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0216885
X-RAY DIFFRACTIONr_bond_other_d0.0010.024664
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9349361
X-RAY DIFFRACTIONr_angle_other_deg0.679311280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4115829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.81123.846351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.748151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2281548
X-RAY DIFFRACTIONr_chiral_restr0.0950.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217750
X-RAY DIFFRACTIONr_gen_planes_other00.021470
X-RAY DIFFRACTIONr_mcbond_it1.10924145
X-RAY DIFFRACTIONr_mcbond_other0.20621668
X-RAY DIFFRACTIONr_mcangle_it2.1536687
X-RAY DIFFRACTIONr_scbond_it3.14742740
X-RAY DIFFRACTIONr_scangle_it5.03662674
LS refinement shellResolution: 2.7→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 123 -
Rwork0.333 2291 -
all-2414 -
obs--100 %
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)
13.13860.4218-1.40754.2076-0.68173.4427-0.11710.033-0.27720.04320.0971-0.20260.23410.380.020.02820.03780.03050.1627-0.01760.137754.9756-7.717226.2967
214.5601-4.93552.18146.90110.94556.1383-0.39880.4602-0.1106-0.2621-0.2534-2.09071.33282.14210.65210.87630.49490.35030.96260.46261.687578.5505-34.670720.6952
34.3240.1242-1.68129.28040.15076.9036-0.450.5544-1.092-0.9946-0.16920.1351.46640.00370.61920.43950.06820.14470.365-0.13220.40964.3701-23.67386.4159
44.0377-1.6939-1.8741.01250.91744.7387-0.0582-0.46860.11130.20730.0981-0.0886-0.01040.1626-0.040.115-0.0493-0.02170.12280.02170.10334.81482.786648.0418
516.6357-2.61773.26348.4908-0.479811.7023-0.1981-1.0814-0.14280.60240.10870.3684-0.0219-1.16070.08940.55660.08820.04510.5978-0.03590.20776.881618.888358.2218
610.9863-1.7424-0.42770.8508-0.2942.40970.27770.4908-0.0082-0.3135-0.13850.0797-0.24150.0167-0.13920.20840.0446-0.01520.05260.01390.042229.18256.018825.3662
73.84090.21591.91673.5992.98048.9958-0.181-0.53120.19070.34070.1454-0.1295-0.31870.06090.03550.19270.0647-0.05550.18150.02770.15919.362323.562942.5514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 197
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 244

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