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- PDB-7qpj: Crystal structure of engineered TCR (756) complexed to HLA-A*02:0... -

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Basic information

Entry
Database: PDB / ID: 7qpj
TitleCrystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • MHC class I antigen
  • Melanoma-associated antigen 10
KeywordsIMMUNE SYSTEM / T-cell receptor / human leukocyte antigen
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 ...antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / 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 iron ion transport / regulation of erythrocyte differentiation / 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 / positive regulation of T cell activation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / histone deacetylase binding / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / positive regulation of protein binding / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / 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
Melanoma-associated antigen 10 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSimister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Adaptimmune Ltd United Kingdom
Citation
Journal: J Immunother Cancer / Year: 2022
Title: Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy.
Authors: Simister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
#1: Journal: Oncoimmunology / Year: 2018
Title: Affinity-enhanced T-cell receptors for adoptive T-cell therapy targeting MAGE-A10: strategy for selection of an optimal candidate.
Authors: Border, E.C. / Sanderson, J.P. / Weissensteiner, T. / Gerry, A.B. / Pumphrey, N.J.
History
DepositionJan 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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
C: MHC class I antigen
D: Beta-2-microglobulin
E: Melanoma-associated antigen 10
A: T-cell receptor alpha chain
B: T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2909
Polymers94,9215
Non-polymers3684
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-52 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.197, 77.446, 116.682
Angle α, β, γ (deg.)90.000, 102.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules CD

#1: Protein MHC class I antigen


Mass: 32082.512 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: Q861F7
#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

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide Melanoma-associated antigen 10 / Cancer/testis antigen 1.10 / CT1.10 / MAGE-10 antigen


Mass: 1035.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43363

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T-cell receptor ... , 2 types, 2 molecules AB

#4: Protein T-cell receptor alpha chain


Mass: 22761.021 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 T-cell receptor beta chain


Mass: 27163.371 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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Non-polymers , 2 types, 532 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Sodium chloride, 0.1M MES pH 6.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.54→77.45 Å / Num. obs: 134415 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.073 / Rrim(I) all: 0.105 / Net I/av σ(I): 6.4 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.43-77.4530.04115.465310.9930.040.05799.4
1.54-1.573.10.98418970.3310.9671.38195.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PBC

7pbc


Resolution: 1.54→64.113 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.468 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2364 6619 4.925 %
Rwork0.2019 127766 -
all0.204 --
obs-134385 96.664 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.768 Å2-0 Å20.149 Å2
2---0.793 Å2-0 Å2
3---1.356 Å2
Refinement stepCycle: LAST / Resolution: 1.54→64.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6470 0 24 528 7022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155950
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6499214
X-RAY DIFFRACTIONr_angle_other_deg1.381.57913697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14221.984383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.894151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8941547
X-RAY DIFFRACTIONr_chiral_restr0.0780.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021670
X-RAY DIFFRACTIONr_nbd_refined0.1980.21055
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.25271
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23085
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2404
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1790.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.213
X-RAY DIFFRACTIONr_nbd_other0.1880.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.210
X-RAY DIFFRACTIONr_mcbond_it2.3412.5743313
X-RAY DIFFRACTIONr_mcbond_other2.342.5733312
X-RAY DIFFRACTIONr_mcangle_it3.5563.854139
X-RAY DIFFRACTIONr_mcangle_other3.5553.8514140
X-RAY DIFFRACTIONr_scbond_it2.9832.8233447
X-RAY DIFFRACTIONr_scbond_other2.9832.8233448
X-RAY DIFFRACTIONr_scangle_it4.5614.1285064
X-RAY DIFFRACTIONr_scangle_other4.564.1285065
X-RAY DIFFRACTIONr_lrange_it6.30629.3797230
X-RAY DIFFRACTIONr_lrange_other6.30529.3817231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.3214960.3399271X-RAY DIFFRACTION95.3529
1.58-1.6230.3424490.3259060X-RAY DIFFRACTION95.4815
1.623-1.670.3284510.3098802X-RAY DIFFRACTION95.3819
1.67-1.7220.3144790.2968533X-RAY DIFFRACTION95.3752
1.722-1.7780.2884440.2698362X-RAY DIFFRACTION96.2404
1.778-1.8410.2643950.2478084X-RAY DIFFRACTION96.0249
1.841-1.910.2624710.2267729X-RAY DIFFRACTION96.2215
1.91-1.9880.2513790.2127611X-RAY DIFFRACTION96.7429
1.988-2.0760.2414130.2147224X-RAY DIFFRACTION96.7566
2.076-2.1780.2623360.2076888X-RAY DIFFRACTION95.8472
2.178-2.2950.2313080.1986655X-RAY DIFFRACTION96.8698
2.295-2.4350.2253090.1856348X-RAY DIFFRACTION97.6959
2.435-2.6030.2272890.1815945X-RAY DIFFRACTION97.5587
2.603-2.8110.22880.1765590X-RAY DIFFRACTION98.7401
2.811-3.0790.2392670.1785102X-RAY DIFFRACTION98.0281
3.079-3.4420.2032420.1764665X-RAY DIFFRACTION98.7324
3.442-3.9740.1931810.1664177X-RAY DIFFRACTION99.0229
3.974-4.8660.2022060.1543488X-RAY DIFFRACTION98.5329
4.866-6.8750.2271320.1962695X-RAY DIFFRACTION97.382
6.875-64.1130.244840.2181537X-RAY DIFFRACTION99.2044

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