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- PDB-8vcl: Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA ... -

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Basic information

Entry
Database: PDB / ID: 8vcl
TitleCrystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Mutant PIK3CA peptide
KeywordsIMMUNE SYSTEM / Peptide-class I Major Histocompatibility Complex / pMHC
Function / homology
Function and homology information


response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / IRS-mediated signalling / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure ...response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / IRS-mediated signalling / autosome genomic imprinting / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / cellular response to hydrostatic pressure / regulation of cellular respiration / positive regulation of protein localization to membrane / Activated NTRK2 signals through PI3K / negative regulation of fibroblast apoptotic process / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / 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 / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / vascular endothelial growth factor signaling pathway / relaxation of cardiac muscle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 1-phosphatidylinositol-3-kinase activity / Golgi medial cisterna / Signaling by ALK / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / PI-3K cascade:FGFR3 / negative regulation of macroautophagy / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / CD8 receptor binding / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / phosphatidylinositol phosphate biosynthetic process / response to dexamethasone / Synthesis of PIPs at the plasma membrane / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / negative regulation of anoikis / RET signaling / protection from natural killer cell mediated cytotoxicity / PI3K events in ERBB2 signaling / protein kinase activator activity / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / intercalated disc / regulation of multicellular organism growth / CD28 dependent PI3K/Akt signaling / 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 / positive regulation of TOR signaling / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / GAB1 signalosome / adipose tissue development / 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 / positive regulation of lamellipodium assembly / energy homeostasis / Signaling by FLT3 ITD and TKD mutants / cardiac muscle contraction / GPVI-mediated activation cascade / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / T cell costimulation / response to muscle stretch / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease
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 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / 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: 2.4 Å
AuthorsMa, J. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118166 United States
CitationJournal: To Be Published
Title: Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide
Authors: Ma, J. / Baker, B.M.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7568
Polymers44,4803
Non-polymers2765
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-18 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.420, 156.420, 85.863
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-540-

HOH

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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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Protein/peptide , 1 types, 1 molecules C

#3: 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: H2L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42336

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Non-polymers , 3 types, 187 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% w/v Polyethylene glycol 3,350, 4% v/v TacsimateTM, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→43.98 Å / Num. obs: 24683 / % possible obs: 97.93 % / Redundancy: 30.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1953 / Rpim(I) all: 0.03545 / Rrim(I) all: 0.1987 / Net I/σ(I): 16.18
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 4.53 / Num. unique obs: 1965 / CC1/2: 0.616 / CC star: 0.873 / Rpim(I) all: 0.1536 / Rrim(I) all: 0.6167 / % possible all: 81.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.98 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 20.1329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 2428 10.01 %
Rwork0.1935 21830 -
obs0.1971 24258 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 18 182 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243225
X-RAY DIFFRACTIONf_angle_d0.49214367
X-RAY DIFFRACTIONf_chiral_restr0.04443
X-RAY DIFFRACTIONf_plane_restr0.0045575
X-RAY DIFFRACTIONf_dihedral_angle_d13.36141184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.2844970.2404868X-RAY DIFFRACTION66.97
2.44-2.50.29361330.24091193X-RAY DIFFRACTION93.98
2.5-2.560.2781420.25261276X-RAY DIFFRACTION98.95
2.56-2.620.29611430.23391293X-RAY DIFFRACTION100
2.62-2.690.25661440.22071289X-RAY DIFFRACTION99.93
2.69-2.770.29471440.22561297X-RAY DIFFRACTION99.86
2.77-2.860.25981430.21481286X-RAY DIFFRACTION100
2.86-2.960.26141440.20961302X-RAY DIFFRACTION99.93
2.96-3.080.2191450.2121298X-RAY DIFFRACTION99.86
3.08-3.220.2421450.20831295X-RAY DIFFRACTION99.93
3.22-3.390.22731450.20091313X-RAY DIFFRACTION99.93
3.39-3.60.23081460.19371305X-RAY DIFFRACTION99.79
3.6-3.880.20311460.17651325X-RAY DIFFRACTION99.73
3.88-4.270.20941480.1561325X-RAY DIFFRACTION99.86
4.27-4.890.1781480.14551341X-RAY DIFFRACTION100
4.89-6.150.18671520.17861366X-RAY DIFFRACTION99.8
6.16-43.980.2461630.19831458X-RAY DIFFRACTION99.69
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)
11.185774804040.32715112465-0.6421854585521.72950428136-0.4412178025261.68304195834-0.06180956182420.06136684233340.08170778419360.1795947761020.2586412341180.1573647974580.0711650909953-0.0497963043574-0.1560005048450.3321264822230.01702924192410.03360408530050.1107317510490.002253906591010.19487066586-66.469152972-7.232813823626.5394115101
21.0964263038-1.11902140116-0.5134698895691.906858361550.83324547880.365956037578-0.142467385013-0.2530071729450.3491327857820.2068723688990.210212421593-0.430812611233-0.200661194922-0.0311215428016-0.4157153220320.961126539110.3851388173370.007895786335320.316142364498-0.05722283182870.404286117269-38.9196694813-29.665220349224.9222517267
30.8483484652750.1072545184670.1383275315171.10324216682-0.01125704554710.0286997314524-0.3477641078970.0213518143556-0.431017889590.05294806018930.1676246426840.1306281848130.5232750913520.0982112500354-0.01355999527430.7817153397430.01366893119430.1232468221010.199809639701-0.03871408426190.368309637639-59.0998523409-30.702188283915.147087443
40.082737558742-0.4991665194310.741975746053.31533504181-4.987276472017.514669169650.0257958934977-0.165433259158-0.04153593516410.4279752825510.6345733370071.05725933059-0.451620986737-0.967287813487-0.6402198653510.3267778091350.009268049274640.08343731072270.304937743590.05616749475740.432840801781-71.220671019-0.80287392433726.4228583206
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 180 )AA1 - 1801 - 180
22chain 'A' and (resid 181 through 274 )AA181 - 274181 - 274
33chain 'B' and (resid 1 through 99 )BB1 - 991 - 99
44chain 'C' and (resid 1 through 9 )CC1 - 91 - 9

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