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- PDB-7pdw: Crystal structure of parent TCR (728) complexed to HLA-A*02:01 pr... -

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Basic information

Entry
Database: PDB / ID: 7pdw
TitleCrystal structure of parent TCR (728) 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 / MAGE-A10
Function / homology
Function and homology information


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 ...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 / 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 / histone deacetylase binding / 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 / 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 / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 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
PHOSPHATE ION / 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: 1.82 Å
AuthorsSimister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: 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.
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 1.2Oct 23, 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
AAA: T-cell receptor alpha chain (TRAV/TRAC)
BBB: T-cell receptor beta chain (TRBV/TRBC)
DDD: Beta-2-microglobulin
EEE: Melanoma-associated antigen 10
FFF: T-cell receptor alpha chain (TRAV/TRAC)
GGG: T-cell receptor beta chain (TRBV/TRBC)
III: Beta-2-microglobulin
JJJ: Melanoma-associated antigen 10
CCC: MHC class I antigen
HHH: MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,28013
Polymers190,00110
Non-polymers2793
Water11,602644
1
AAA: T-cell receptor alpha chain (TRAV/TRAC)
BBB: T-cell receptor beta chain (TRBV/TRBC)
DDD: Beta-2-microglobulin
EEE: Melanoma-associated antigen 10
CCC: MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1857
Polymers95,0015
Non-polymers1842
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-54 kcal/mol
Surface area36660 Å2
MethodPISA
2
FFF: T-cell receptor alpha chain (TRAV/TRAC)
GGG: T-cell receptor beta chain (TRBV/TRBC)
III: Beta-2-microglobulin
JJJ: Melanoma-associated antigen 10
HHH: MHC class I antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0956
Polymers95,0015
Non-polymers951
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-61 kcal/mol
Surface area36730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.081, 95.834, 106.261
Angle α, β, γ (deg.)109.170, 96.510, 99.700
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21FFF
32BBB
42GGG
53DDD
63III
74CCC
84HHH

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
111LYSLYSSERSERAAAA3 - 2023 - 202
221LYSLYSSERSERFFFE3 - 2023 - 202
332GLYGLYARGARGBBBB4 - 2394 - 239
442GLYGLYARGARGGGGF4 - 2394 - 239
553METMETMETMETDDDC1 - 1001 - 100
663METMETMETMETIIIG1 - 1001 - 100
774GLYGLYPROPROCCCI2 - 2772 - 277
884GLYGLYPROPROHHHJ2 - 2772 - 277

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8

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Components

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T-cell receptor ... , 2 types, 4 molecules AAAFFFBBBGGG

#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)

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Protein , 2 types, 4 molecules DDDIIICCCHHH

#3: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
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
#5: Protein MHC class I antigen


Mass: 32082.512 Da / Num. of mol.: 2
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

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Protein/peptide , 1 types, 2 molecules EEEJJJ

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


Mass: 1035.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Melanoma-associated antigen 10 / Source: (synth.) Homo sapiens (human) / References: UniProt: P43363

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Non-polymers , 3 types, 647 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 644 / 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: 2.6572 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

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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: 1.82→98.71 Å / Num. obs: 158062 / % possible obs: 90.2 % / Redundancy: 1.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.098 / Rrim(I) all: 0.139 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.97-98.711.50.03511.110410.9320.0350.04997.3
1.82-1.851.40.6720.776340.4640.6720.95

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Processing

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

7pbc


Resolution: 1.82→81.936 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.004 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 8035 5.084 %Random selection
Rwork0.2013 150025 --
all0.203 ---
obs0.2028 158060 90.166 %-
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: 36.993 Å2
Baniso -1Baniso -2Baniso -3
1--2.023 Å20.947 Å20.098 Å2
2--2.143 Å20.857 Å2
3----0.991 Å2
Refinement stepCycle: LAST / Resolution: 1.82→81.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13024 0 17 644 13685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313465
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711824
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.64918332
X-RAY DIFFRACTIONr_angle_other_deg1.2771.57827222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62251646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68422.109773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33152066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9231593
X-RAY DIFFRACTIONr_chiral_restr0.0670.21709
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023324
X-RAY DIFFRACTIONr_nbd_refined0.1970.22144
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.210751
X-RAY DIFFRACTIONr_nbtor_refined0.1640.26232
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2649
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.213
X-RAY DIFFRACTIONr_nbd_other0.1840.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.29
X-RAY DIFFRACTIONr_mcbond_it2.9123.8326585
X-RAY DIFFRACTIONr_mcbond_other2.913.8316584
X-RAY DIFFRACTIONr_mcangle_it4.3755.7368217
X-RAY DIFFRACTIONr_mcangle_other4.3765.7368218
X-RAY DIFFRACTIONr_scbond_it3.394.1256880
X-RAY DIFFRACTIONr_scbond_other3.3784.1236876
X-RAY DIFFRACTIONr_scangle_it5.2456.06310110
X-RAY DIFFRACTIONr_scangle_other5.2386.0610104
X-RAY DIFFRACTIONr_lrange_it7.27342.89714358
X-RAY DIFFRACTIONr_lrange_other7.26542.82114251
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.055666
X-RAY DIFFRACTIONr_ncsr_local_group_20.0780.057355
X-RAY DIFFRACTIONr_ncsr_local_group_30.0650.053013
X-RAY DIFFRACTIONr_ncsr_local_group_40.0910.058785
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.079350.05009
12FFFX-RAY DIFFRACTIONLocal ncs0.079350.05009
23BBBX-RAY DIFFRACTIONLocal ncs0.078080.0501
24GGGX-RAY DIFFRACTIONLocal ncs0.078080.0501
35DDDX-RAY DIFFRACTIONLocal ncs0.065420.0501
36IIIX-RAY DIFFRACTIONLocal ncs0.065420.0501
47CCCX-RAY DIFFRACTIONLocal ncs0.090950.05009
48HHHX-RAY DIFFRACTIONLocal ncs0.090950.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8670.3355470.33710865X-RAY DIFFRACTION87.522
1.867-1.9180.3495770.32910715X-RAY DIFFRACTION89.4841
1.918-1.9740.3135410.310348X-RAY DIFFRACTION89.0424
1.974-2.0350.2975240.2710108X-RAY DIFFRACTION88.7924
2.035-2.1010.2665540.2649861X-RAY DIFFRACTION90.22
2.101-2.1750.2494860.239634X-RAY DIFFRACTION90.0436
2.175-2.2570.2664740.2369151X-RAY DIFFRACTION89.2609
2.257-2.3490.2514540.2178846X-RAY DIFFRACTION89.3114
2.349-2.4540.2494780.2048366X-RAY DIFFRACTION88.8755
2.454-2.5730.234050.198215X-RAY DIFFRACTION90.8325
2.573-2.7120.2434220.1967685X-RAY DIFFRACTION89.6296
2.712-2.8770.233940.1897314X-RAY DIFFRACTION90.0888
2.877-3.0750.233900.1826976X-RAY DIFFRACTION91.6968
3.075-3.3210.2133830.1866638X-RAY DIFFRACTION93.6633
3.321-3.6380.2143550.1876040X-RAY DIFFRACTION92.6409
3.638-4.0670.1953040.1685484X-RAY DIFFRACTION92.8159
4.067-4.6950.1812800.1444824X-RAY DIFFRACTION93.2578
4.695-5.7460.1842070.1654026X-RAY DIFFRACTION91.465
5.746-8.1130.221580.1963104X-RAY DIFFRACTION90.4603
8.113-81.9360.1711020.1731826X-RAY DIFFRACTION97.0307

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