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- PDB-7pdx: Crystal structure of parent MAGE-A10 TCR (728) -

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Basic information

Entry
Database: PDB / ID: 7pdx
TitleCrystal structure of parent MAGE-A10 TCR (728)
Components
  • T-cell receptor alpha chain (TRAV/TRAC)
  • T-cell receptor beta chain (TRBV/TRBC)
KeywordsIMMUNE SYSTEM / T-cell receptor / immunoglobulin fold
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSimister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private 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
DepositionAug 9, 2021Deposition 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 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
CCC: T-cell receptor alpha chain (TRAV/TRAC)
DDD: T-cell receptor beta chain (TRBV/TRBC)
AAA: T-cell receptor alpha chain (TRAV/TRAC)
BBB: T-cell receptor beta chain (TRBV/TRBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1737
Polymers100,0074
Non-polymers1663
Water5,386299
1
CCC: T-cell receptor alpha chain (TRAV/TRAC)
DDD: T-cell receptor beta chain (TRBV/TRBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0393
Polymers50,0032
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-41 kcal/mol
Surface area19760 Å2
MethodPISA
2
AAA: T-cell receptor alpha chain (TRAV/TRAC)
BBB: T-cell receptor beta chain (TRBV/TRBC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1344
Polymers50,0032
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-36 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.930, 59.171, 86.020
Angle α, β, γ (deg.)101.940, 105.870, 104.690
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CCC
21AAA
32DDD
42BBB

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPROPROCCCA3 - 2013 - 201
221LYSLYSPROPROAAAC3 - 2013 - 201
332GLYGLYALAALADDDB4 - 2404 - 240
442GLYGLYALAALABBBD4 - 2404 - 240

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein T-cell receptor alpha chain (TRAV/TRAC)


Mass: 22818.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein T-cell receptor beta chain (TRBV/TRBC)


Mass: 27185.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
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: 2.486 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M PCTP pH 7.0, 25% w/v PEG 1500

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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: 2.27→79.011 Å / Num. obs: 38348 / % possible obs: 86.2 % / Redundancy: 1.5 % / Biso Wilson estimate: 14.61 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.117 / Rrim(I) all: 0.166 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.08-79.011.60.0726.16570.9840.0720.10194.4
2.27-2.341.50.212.334710.8980.210.29785

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.2data scaling
MOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PDW

7pdw


Resolution: 2.27→79.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.608 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.432 / ESU R Free: 0.269
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 1873 4.886 %Random
Rwork0.192 36462 --
all0.195 ---
obs-38335 86.177 %-
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: 32.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.721 Å21.047 Å2-0.062 Å2
2--2.877 Å2-0.526 Å2
3----2.822 Å2
Refinement stepCycle: LAST / Resolution: 2.27→79.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 7 299 7050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136936
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176132
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6459451
X-RAY DIFFRACTIONr_angle_other_deg1.251.57614115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2345873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76222.818362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.399151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.911538
X-RAY DIFFRACTIONr_chiral_restr0.0640.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021679
X-RAY DIFFRACTIONr_nbd_refined0.1890.21120
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25682
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23225
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2332
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3710.228
X-RAY DIFFRACTIONr_nbd_other0.250.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_mcbond_it2.8463.4283501
X-RAY DIFFRACTIONr_mcbond_other2.8453.4273500
X-RAY DIFFRACTIONr_mcangle_it4.3365.1314371
X-RAY DIFFRACTIONr_mcangle_other4.3365.1324372
X-RAY DIFFRACTIONr_scbond_it3.3173.6713435
X-RAY DIFFRACTIONr_scbond_other3.3133.6723432
X-RAY DIFFRACTIONr_scangle_it5.1115.3875080
X-RAY DIFFRACTIONr_scangle_other5.1125.3885075
X-RAY DIFFRACTIONr_lrange_it7.15839.3957282
X-RAY DIFFRACTIONr_lrange_other7.14239.3767256
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.055503
X-RAY DIFFRACTIONr_ncsr_local_group_20.0740.057461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11CCCX-RAY DIFFRACTIONLocal ncs0.110520.05009
12AAAX-RAY DIFFRACTIONLocal ncs0.110520.05009
23DDDX-RAY DIFFRACTIONLocal ncs0.073750.0501
24BBBX-RAY DIFFRACTIONLocal ncs0.073750.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.27-2.3290.3191470.25526490.25833100.7770.8184.47130.263
2.329-2.3930.3251400.2326450.23532180.8080.84386.54440.236
2.393-2.4620.3341160.22725040.23230900.830.85784.78960.233
2.462-2.5380.3431420.2224400.22630260.8010.85785.32720.229
2.538-2.6210.2481220.21522720.21629040.8670.87482.4380.228
2.621-2.7130.331210.25722510.2628670.740.83682.73460.266
2.713-2.8150.297940.21823020.22127290.8250.87887.79770.235
2.815-2.930.26980.1821610.18326560.8870.91885.05270.197
2.93-3.060.2631180.18420060.18925140.890.9284.48690.205
3.06-3.2090.2581210.18319490.18724030.8910.92886.14230.204
3.209-3.3820.2491160.18418930.18822870.9050.91787.84430.207
3.382-3.5870.246840.2118520.21221780.8750.89888.88890.239
3.587-3.8340.255910.19617100.19820560.8870.91587.59730.227
3.834-4.140.212820.1715810.17318970.9470.94587.66470.199
4.14-4.5340.165610.13115310.13217700.9610.96689.94350.161
4.534-5.0670.151610.13613540.13715720.9670.97190.01270.173
5.067-5.8470.232550.1911820.19214010.9380.95388.29410.231
5.847-7.1520.296450.2239640.22611720.8880.92786.09210.27
7.152-10.0730.225400.1787650.1819210.9310.94487.4050.234
10.073-79.0110.27190.2394500.2415010.9280.90993.61280.29

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