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- PDB-7rrg: Crystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in c... -

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Basic information

Entry
Database: PDB / ID: 7rrg
TitleCrystal structure of human 0606T1-2 TCR bound to HLA-A*03:01 in complex with a mutant PIK3CA peptide
Components
  • (T cell receptor, ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Mutant PIK3CA peptide
KeywordsIMMUNE SYSTEM / T cell receptor / peptide major histocompatibility complex
Function / homology
Function and homology information


response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / response to butyrate / IRS-mediated signalling / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / autosome genomic imprinting ...response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to L-leucine / response to butyrate / IRS-mediated signalling / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / autosome genomic imprinting / regulation of cellular respiration / Activated NTRK2 signals through PI3K / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / positive regulation of protein localization to membrane / vasculature development / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / Signaling by LTK in cancer / anoikis / phosphatidylinositol-3-phosphate biosynthetic process / Signaling by LTK / MET activates PI3K/AKT signaling / relaxation of cardiac muscle / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / phosphatidylinositol 3-kinase / 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 / 1-phosphatidylinositol-3-kinase activity / positive regulation of CD8-positive, alpha-beta T cell proliferation / Signaling by ALK / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of macroautophagy / PI-3K cascade:FGFR2 / response to dexamethasone / PI-3K cascade:FGFR4 / phosphatidylinositol-mediated signaling / CD8 receptor binding / PI-3K cascade:FGFR1 / antigen processing and presentation of exogenous peptide antigen via MHC class I / phosphatidylinositol phosphate biosynthetic process / beta-2-microglobulin binding / Synthesis of PIPs at the plasma membrane / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / RET signaling / protection from natural killer cell mediated cytotoxicity / negative regulation of anoikis / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / insulin receptor substrate binding / intercalated disc / 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 / regulation of multicellular organism growth / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / Interleukin receptor SHC signaling / positive regulation of TOR signaling / Role of phospholipids in phagocytosis / protein kinase activator activity / adipose tissue development / GAB1 signalosome / phagocytosis / endothelial cell migration / detection of bacterium / T cell receptor binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by FGFR4 in disease / energy homeostasis / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / cardiac muscle contraction / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / response to muscle stretch / Signaling by FGFR2 in disease / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of smooth muscle cell proliferation
Similarity search - Function
PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain ...PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / C2 domain superfamily / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMa, J. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129543 United States
CitationJournal: Nat Med / Year: 2022
Title: Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA.
Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / ...Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / Bestman, W.D. / Da Cruz Paula, A. / Aricescu, I.S. / Drilon, A. / Betel, D. / Scheinberg, D.A. / Baker, B.M. / Klebanoff, C.A.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value
Revision 1.2May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
D: T cell receptor, alpha chain
E: T cell receptor, beta chain
C: Mutant PIK3CA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,28518
Polymers95,0885
Non-polymers1,19713
Water7,458414
1
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide
hetero molecules

D: T cell receptor, alpha chain
E: T cell receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,28518
Polymers95,0885
Non-polymers1,19713
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area13530 Å2
ΔGint-51 kcal/mol
Surface area36660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.270, 46.253, 120.262
Angle α, β, γ (deg.)90.000, 118.670, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31628.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P04439
#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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T cell receptor, ... , 2 types, 2 molecules DE

#3: Protein T cell receptor, alpha chain


Mass: 22922.492 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)
#4: Protein T cell receptor, beta chain


Mass: 27684.998 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

#5: Protein/peptide Mutant PIK3CA peptide / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase ...Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / p110alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 972.098 Da / Num. of mol.: 1 / Mutation: H1047L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42336

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Non-polymers , 2 types, 427 molecules

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


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% w/v Polyethylene glycol 3,350, 100 mM Succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 61648 / % possible obs: 98.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 29.13 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.048 / Rrim(I) all: 0.122 / Net I/σ(I): 17.92
Reflection shellResolution: 2.12→2.16 Å / Rmerge(I) obs: 0.614 / Num. unique obs: 2969 / CC1/2: 0.812 / CC star: 0.947 / Rpim(I) all: 0.284 / Rrim(I) all: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPG, 6AT6, 6R2L

2xpg

6at6

6r2l


Resolution: 2.12→49.85 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 5965 9.98 %
Rwork0.1925 53795 -
obs0.1954 59760 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.17 Å2 / Biso mean: 55.0541 Å2 / Biso min: 13.39 Å2
Refinement stepCycle: final / Resolution: 2.12→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 78 414 6894
Biso mean--52.9 41.43 -
Num. residues----803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.12-2.150.2671490.25231435158476
2.15-2.170.30771710.23691649182088
2.17-2.20.28481880.22661691187989
2.2-2.230.22742070.21761671187891
2.23-2.250.24131810.2241693187491
2.25-2.290.27061940.22181723191792
2.29-2.320.24812010.21651777197894
2.32-2.350.2351770.20691737191493
2.35-2.390.2492020.2111770197294
2.39-2.430.24811990.20291774197394
2.43-2.470.24552030.20881778198195
2.47-2.520.24731990.21591768196795
2.52-2.560.24242060.21631765197193
2.56-2.620.23921820.22581681186391
2.62-2.670.24471940.22561822201697
2.67-2.740.2782120.21981837204997
2.74-2.80.25912020.21521815201798
2.8-2.880.24421900.19861879206998
2.88-2.960.22672150.19511841205698
2.96-3.060.23962150.19771863207899
3.06-3.170.25462030.1921850205399
3.17-3.30.23172040.20251903210799
3.3-3.450.23842040.19551837204198
3.45-3.630.21621970.17751855205298
3.63-3.860.20841990.17241804200394
3.86-4.150.18142090.164219042113100
4.15-4.570.16862140.152618922106100
4.57-5.230.17622140.154819192133100
5.23-6.590.19932130.19551891210498
6.59-49.850.20942210.20221971219298
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)
11.7627-0.1617-0.46892.0481-0.37571.16440.0878-0.22310.24960.0292-0.03720.1814-0.13950.13160.02360.1917-0.0293-0.00240.0982-0.02320.265428.46831.21345.8451
21.1882-1.0904-0.01592.1005-0.46881.5640.0931-1.093-0.12550.92430.15090.13570.555-0.0891-0.0210.7177-0.11010.03520.8174-0.02830.21898.6056-4.068334.5896
33.4733-0.1889-0.4042.25880.04273.00580.036-0.07-0.24440.0227-0.07130.41350.0261-0.34380.03150.1830.001-0.00240.1233-0.00220.27283.7282-7.267312.8895
42.1708-0.0772-0.51512.0214-0.56441.2930.3177-0.06220.70210.10180.1360.1425-0.3439-0.247-0.27170.24840.07090.03080.2190.01260.393960.6628-11.87989.9669
50.2574-0.74540.163.25112.25916.89780.2656-1.18070.70050.43770.23010.1167-0.54280.0845-0.13530.71830.04370.43261.2171-0.22040.92942.3113-8.310336.7957
60.5160.0033-0.10350.00490.050.94970.0774-1.1010.86120.43940.0771-0.127-0.30950.2478-0.0920.4859-0.0102-0.04480.6952-0.36470.50879.514-11.283524.0682
70.6271-0.2419-0.29861.14560.3142.02530.2004-0.56910.32060.43980.1805-0.1168-0.04870.27390.15240.92480.02340.21221.4313-0.25710.408257.1784-13.642844.6777
84.9334-5.4993-3.10157.51762.18143.54710.1516-0.28070.2734-0.34690.037-0.1371-0.21240.3359-0.17390.1656-0.0487-0.04760.09440.00140.186234.94611.07751.0347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )A1 - 180
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 274 )A181 - 274
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 99 )B0 - 99
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 113 )D4 - 113
5X-RAY DIFFRACTION5chain 'D' and (resid 114 through 193 )D114 - 193
6X-RAY DIFFRACTION6chain 'E' and (resid 3 through 115 )E3 - 115
7X-RAY DIFFRACTION7chain 'E' and (resid 116 through 242 )E116 - 242
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 9 )C1 - 9

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