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- PDB-6tmo: Structure determination of an enhanced affinity TCR, a24b17, in c... -

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Basic information

Entry
Database: PDB / ID: 6tmo
TitleStructure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01 presenting a MART-1 peptide, EAAGIGILTV
Components
  • Alpha chain of engineered high affinity T-cell receptor
  • Beta chain of high affinity engineered T-cell receptor
  • Beta-2-microglobulin
  • EAAGIGILTV
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / High affinity / T-cell receptor
Function / homology
Function and homology information


melanosome membrane / Regulation of MITF-M-dependent genes involved in pigmentation / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway ...melanosome membrane / Regulation of MITF-M-dependent genes involved in pigmentation / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / melanosome / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Protein melan-A / Protein melan-A / 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 / : ...Protein melan-A / Protein melan-A / 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
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Mol Ther Oncolytics / Year: 2020
Title: Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy.
Authors: Crean, R.M. / MacLachlan, B.J. / Madura, F. / Whalley, T. / Rizkallah, P.J. / Holland, C.J. / McMurran, C. / Harper, S. / Godkin, A. / Sewell, A.K. / Pudney, C.R. / van der Kamp, M.W. / Cole, D.K.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: EAAGIGILTV
D: Alpha chain of engineered high affinity T-cell receptor
E: Beta chain of high affinity engineered T-cell receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,91725
Polymers94,0525
Non-polymers1,86520
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-81 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.490, 121.490, 82.680
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 , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen


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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein Alpha chain of engineered high affinity T-cell receptor


Mass: 21887.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein Beta chain of high affinity engineered T-cell receptor


Mass: 27391.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide EAAGIGILTV


Mass: 943.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655*PLUS

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Non-polymers , 5 types, 408 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 0.2 M Ammonium Sulphate 15 % PEG 4000 8.7% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→54.332 Å / Num. obs: 69920 / % possible obs: 99.4 % / Redundancy: 8.3 % / Biso Wilson estimate: 33.3 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.096 / Rsym value: 0.084 / Net I/av σ(I): 7.8 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.158.40.71314282951100.2770.8070.7133.699
2.15-2.218.40.5941.24202350000.2290.670.5944.399.1
2.21-2.288.40.5071.44052448400.1970.5740.507599.2
2.28-2.358.40.4171.83995047470.1620.4730.4175.999.1
2.35-2.428.40.36623885146110.1420.4150.3666.699.1
2.42-2.518.40.2912.53728944290.1130.330.291899.2
2.51-2.68.40.2333.23607542920.0910.2640.2339.699.6
2.6-2.718.30.1953.83444141300.0760.2210.19511.299.6
2.71-2.838.40.1554.83333139820.060.1760.15513.299.6
2.83-2.978.40.1236.13210538190.0480.1390.1231699.4
2.97-3.138.40.09383027836220.0360.1050.09319.399.7
3.13-3.328.30.0759.82834734170.0290.0850.07522.999.7
3.32-3.558.20.06211.72646432220.0240.070.0622799.8
3.55-3.838.20.05313.22468130180.0210.060.0533199.8
3.83-4.28.20.04714.12270527800.0180.0520.04734.299.8
4.2-4.780.0415.72015225080.0160.0440.0437.299.9
4.7-5.428.20.03717.31829622400.0140.0410.03737.8100
5.42-6.648.30.03917.21560718860.0150.0440.03937.1100
6.64-9.3980.03319.91175814670.0130.0370.03338.399.5
9.39-54.3327.40.02922.759118000.0120.0330.02939.395.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å54.33 Å
Translation2.5 Å54.33 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGI

3hgi


Resolution: 2.1→54.33 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.782 / SU ML: 0.093 / SU R Cruickshank DPI: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 3532 5.1 %RANDOM
Rwork0.1725 ---
obs0.1744 66386 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 180.17 Å2 / Biso mean: 40.285 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.1→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 116 388 7132
Biso mean--55.61 43.39 -
Num. residues----827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216952
X-RAY DIFFRACTIONr_bond_other_d0.0010.024754
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9419431
X-RAY DIFFRACTIONr_angle_other_deg0.746311484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6465828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00723.846351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.974151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7381548
X-RAY DIFFRACTIONr_chiral_restr0.1290.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217748
X-RAY DIFFRACTIONr_gen_planes_other00.021471
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 254 -
Rwork0.216 4845 -
all-5099 -
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)
12.7702-0.00450.24112.03990.84922.09550.01570.03880.09010.0114-0.01260.106-0.1589-0.1223-0.0030.11070.00780.02370.0167-0.01440.0574-7.787154.816156.9185
24.8688-2.4819-0.14838.0270.98586.2015-0.1706-0.11171.5814-0.5214-0.36940.3454-1.6062-0.81530.540.53130.2342-0.28370.4735-0.27330.98-34.273478.733562.063
35.54520.94290.52392.98581.70175.1228-0.0396-0.71010.05580.2564-0.39220.63030.1557-1.21690.43180.15-0.00280.04470.368-0.11720.2409-23.63164.229576.8703
41.4269-0.9798-0.52593.35020.7533.27340.05160.2050.0637-0.3487-0.059-0.0888-0.108-0.02630.00740.0727-0.0114-0.01840.0360.00770.06372.910634.808835.2926
57.13250.4573-1.098210.8827-4.75588.36430.22540.1687-0.4183-0.9564-0.4063-0.14671.06470.09060.18090.72130.15080.05590.3908-0.0030.265419.45886.874125.3428
61.0216-1.84420.29336.25930.54331.6309-0.1452-0.2058-0.04420.50520.1734-0.02090.05340.0982-0.02820.09360.0193-0.02350.1099-0.0030.06336.18929.167157.8064
73.1598-0.2581-1.48554.4412-2.23676.88470.28490.44220.1123-0.7961-0.3587-0.28650.01920.26580.07380.23020.12020.01950.15550.06220.186623.93719.49841.0971
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 - 200
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 246

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