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- PDB-9asg: Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA ... -

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Basic information

Entry
Database: PDB / ID: 9asg
TitleCrystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide analogue (Trp-6 Bta)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
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 / regulation of actin filament organization / response to L-leucine / 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 / regulation of actin filament organization / response to L-leucine / 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 / 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 / anoikis / Signaling by LTK in cancer / phosphatidylinositol-3-phosphate biosynthetic process / relaxation of cardiac muscle / 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 / 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 / 1-phosphatidylinositol-3-kinase activity / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Signaling by ALK / positive regulation of CD8-positive, alpha-beta T cell proliferation / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of macroautophagy / response to dexamethasone / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / CD8 receptor binding / PI-3K cascade:FGFR1 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / endoplasmic reticulum exit site / energy homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / RET signaling / negative regulation of anoikis / protection from natural killer cell mediated cytotoxicity / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / intercalated disc / protein kinase activator activity / regulation of multicellular organism growth / 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 / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / GAB1 signalosome / adipose tissue development / phagocytosis / endothelial cell migration / detection of bacterium / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / T cell receptor binding / Signaling by FGFR4 in disease / positive regulation of lamellipodium assembly / cardiac muscle contraction / GPVI-mediated activation cascade / 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 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
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: 2.03 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: Nat Commun / Year: 2025
Title: Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.
Authors: Ma, J. / Ayres, C.M. / Brambley, C.A. / Chandran, S.S. / Rosales, T.J. / Perera, W.W.J.G. / Eldaly, B. / Murray, W.T. / Corcelli, S.A. / Kovrigin, E.L. / Klebanoff, C.A. / Baker, B.M.
History
DepositionFeb 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5894
Polymers44,4973
Non-polymers921
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-13 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.800, 156.800, 85.602
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

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Components

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


Mass: 31628.838 Da / Num. of mol.: 1 / Fragment: extracellular domain
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
#3: Protein/peptide Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / ...PI3-kinase subunit alpha / PI3K-alpha / PI3Kalpha / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / PtdIns-3-kinase subunit p110-alpha / p110alpha / Phosphoinositide 3-kinase alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 989.149 Da / Num. of mol.: 1 / Fragment: residues 1046-1054 (Uniprot numbering) / Mutation: H2L, W6Bta / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P42336, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 15% w/v Polyethylene glycol 3,350, 150mM Cesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.03→44.02 Å / Num. obs: 40437 / % possible obs: 97.22 % / Redundancy: 34.1 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2017 / Rpim(I) all: 0.03568 / Rrim(I) all: 0.205 / Net I/σ(I): 25.73
Reflection shellResolution: 2.03→2.103 Å / Rmerge(I) obs: 1.548 / Mean I/σ(I) obs: 3.72 / Num. unique obs: 3563 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.315 / % possible all: 89.88

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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: 2.03→44.02 Å / SU ML: 0.2136 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 22.9186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 3913 9.88 %
Rwork0.2027 35675 -
obs0.2062 39588 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.38 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 6 402 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263215
X-RAY DIFFRACTIONf_angle_d0.62384357
X-RAY DIFFRACTIONf_chiral_restr0.0417443
X-RAY DIFFRACTIONf_plane_restr0.0046574
X-RAY DIFFRACTIONf_dihedral_angle_d14.49761193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.29721250.27911106X-RAY DIFFRACTION85.72
2.05-2.080.31161270.27071150X-RAY DIFFRACTION89.36
2.08-2.10.29371230.2651193X-RAY DIFFRACTION92.55
2.1-2.130.25661260.24871213X-RAY DIFFRACTION94.16
2.13-2.160.32111360.26321229X-RAY DIFFRACTION96.06
2.16-2.190.2981380.25231274X-RAY DIFFRACTION96.84
2.19-2.230.26141330.25731166X-RAY DIFFRACTION91.29
2.23-2.270.3331350.28491223X-RAY DIFFRACTION94.57
2.27-2.30.29561270.26061159X-RAY DIFFRACTION90.31
2.3-2.350.2511350.24551271X-RAY DIFFRACTION98.05
2.35-2.390.30851410.23421274X-RAY DIFFRACTION98.13
2.39-2.440.28061420.21311278X-RAY DIFFRACTION98.68
2.44-2.490.27281410.21711283X-RAY DIFFRACTION99.37
2.49-2.550.28181430.231290X-RAY DIFFRACTION99.24
2.55-2.620.28071410.22721280X-RAY DIFFRACTION99.02
2.62-2.690.25391450.21361300X-RAY DIFFRACTION99.52
2.69-2.770.25661410.2181303X-RAY DIFFRACTION99.45
2.77-2.850.22271410.20911288X-RAY DIFFRACTION99.44
2.85-2.960.23651450.2141305X-RAY DIFFRACTION99.79
2.96-3.070.22341440.2041316X-RAY DIFFRACTION99.86
3.07-3.210.25711440.20151304X-RAY DIFFRACTION99.86
3.21-3.380.2261440.1851317X-RAY DIFFRACTION100
3.38-3.60.22671450.1821319X-RAY DIFFRACTION99.93
3.6-3.870.19741420.15941298X-RAY DIFFRACTION96.97
3.88-4.260.18761470.1531332X-RAY DIFFRACTION100
4.26-4.880.17461480.13831351X-RAY DIFFRACTION100
4.88-6.140.19691520.18161380X-RAY DIFFRACTION100
6.15-44.020.2331620.21531473X-RAY DIFFRACTION99.88
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)
10.4409856549130.0799481874671-0.1871870155510.864877929628-0.2217563092380.576583275847-0.04407539864940.02040849196790.1083596982430.1443152170380.1802290838710.1599210790280.0076054367437-0.08623668312760.0837407922160.327381041183-0.01142021455230.03776356188460.08798008325740.03417434352050.18178435368-66.6726675529-7.2655901594826.4289641996
21.43362812422-1.27612587109-0.7675754113282.319090070131.158861843060.6402748537420.00800614319878-0.1708583317190.4096744250810.01798177837780.15132316962-0.559681585927-0.07213568244750.0696394660289-0.3214006510680.7541090167960.293882310485-0.0352321578960.379203316216-0.05950629045260.413208096798-39.1252722895-29.792412900624.7909758452
30.989858825412-0.1637064124460.2090228122671.758552172570.04626342225530.389699789525-0.1889251648630.0345769658311-0.3686339356370.05113621513920.08202530925830.135877470780.315216415410.05350240564140.003963237619690.60737478388-0.005685527336740.08893406296410.171105705765-0.03822063102320.271864262525-59.2565593399-30.692907697514.998916666
40.185509313581-0.09111036043720.07729869423170.1251922751460.1452353846280.449450251389-0.05128619721870.2163530281460.270380972252-0.02939972869580.2381399783380.615221549695-0.54352768354-0.297838899975-0.1903202850170.4525030206910.04801055182550.04403455472050.2275561795690.1431878952610.432960628191-71.5382025587-0.82001003145226.4784549139
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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