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- PDB-9cmv: Crystal structure of the KRAS-p110alpha complex in the presence o... -

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Basic information

Entry
Database: PDB / ID: 9cmv
TitleCrystal structure of the KRAS-p110alpha complex in the presence of molecular glue D223
Components
  • GTPase KRas
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
KeywordsONCOPROTEIN / RAS / KRAS / PI3Kalpha / p110alpha / PIK3CA / inducer compound
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 / autosome genomic imprinting / cellular response to hydrostatic pressure ...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 / autosome genomic imprinting / 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 / Signaling by LTK in cancer / anoikis / 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 / response to mineralocorticoid / GMP binding / 1-phosphatidylinositol-3-kinase activity / forebrain astrocyte development / Signaling by ALK / LRR domain binding / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / regulation of synaptic transmission, GABAergic / negative regulation of macroautophagy / negative regulation of epithelial cell differentiation / PI-3K cascade:FGFR2 / response to dexamethasone / response to isolation stress / PI-3K cascade:FGFR4 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / phosphatidylinositol phosphate biosynthetic process / Rac protein signal transduction / Synthesis of PIPs at the plasma membrane / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / RET signaling / negative regulation of anoikis / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / PI3K Cascade / RUNX3 regulates p14-ARF / intercalated disc / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / regulation of multicellular organism growth / Activated NTRK2 signals through RAS / protein kinase activator activity / CD28 dependent PI3K/Akt signaling / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / RAC2 GTPase cycle / Interleukin receptor SHC signaling / positive regulation of TOR signaling / Role of phospholipids in phagocytosis / cardiac muscle cell proliferation / Signalling to RAS / GAB1 signalosome / adipose tissue development / phagocytosis / endothelial cell migration / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants
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 / Small GTPase, Ras-type / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsCzyzyk, D.J. / Yan, W. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: Science / Year: 2025
Title: Molecular glues that facilitate RAS binding to PI3K alpha promote glucose uptake without insulin.
Authors: Terayama, K. / Furuzono, S. / Fer, N. / Yan, W. / Young, L.C. / Czyzyk, D.J. / Goldstein de Salazar, R. / Sasaki, M. / Uozumi, A. / Konishi, M. / Kanda, S. / Sogawa, Y. / Yamaguchi, M. / ...Authors: Terayama, K. / Furuzono, S. / Fer, N. / Yan, W. / Young, L.C. / Czyzyk, D.J. / Goldstein de Salazar, R. / Sasaki, M. / Uozumi, A. / Konishi, M. / Kanda, S. / Sogawa, Y. / Yamaguchi, M. / Tsuji, T. / Kuroyanagi, J. / Hayashi, M. / Ogura, Y. / Simanshu, D.K. / Kubota, K. / Tanaka, J. / McCormick, F.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6998
Polymers131,3622
Non-polymers1,3376
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.478, 127.340, 190.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein 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: 112033.430 Da / Num. of mol.: 1 / Mutation: W1057A/I1058A/F1059A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CA / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P42336, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19328.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116

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Non-polymers , 5 types, 11 molecules

#3: Chemical ChemComp-A1AZD / tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate


Mass: 581.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32FN5O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, 0.1 M NaCl, 10 % PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.01→56.9 Å / Num. obs: 28580 / % possible obs: 98.1 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
3.01-3.194.51.0451.5145800.7198.7
3.19-3.414.20.6212.6142690.86198.2
3.41-3.684.50.3665.240220.93198.3
3.68-4.034.80.2029.4836860.96298.8
4.03-4.514.60.11314.0933870.98798.6
4.51-5.24.30.07618.5729510.99397.6
5.2-6.374.70.07419.8525560.99397.8
6.37-8.974.40.0525.6119640.99796.7
8.97-56.940.03336.511650.99894.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→56.9 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1998 7 %
Rwork0.2314 --
obs0.234 28560 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.01→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8354 0 87 5 8446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028619
X-RAY DIFFRACTIONf_angle_d0.39411693
X-RAY DIFFRACTIONf_dihedral_angle_d11.4663178
X-RAY DIFFRACTIONf_chiral_restr0.0391299
X-RAY DIFFRACTIONf_plane_restr0.0031499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.080.40971430.35091898X-RAY DIFFRACTION99
3.08-3.170.3771380.36511862X-RAY DIFFRACTION99
3.17-3.260.42581420.39121883X-RAY DIFFRACTION98
3.26-3.370.45321390.4321837X-RAY DIFFRACTION98
3.37-3.490.47311410.36191884X-RAY DIFFRACTION98
3.49-3.630.37091410.29171868X-RAY DIFFRACTION98
3.63-3.790.28611410.23871883X-RAY DIFFRACTION99
3.79-3.990.27881450.25961917X-RAY DIFFRACTION99
3.99-4.240.2681430.22481902X-RAY DIFFRACTION98
4.24-4.570.24221420.18251888X-RAY DIFFRACTION99
4.57-5.030.19071430.17831891X-RAY DIFFRACTION98
5.03-5.750.23511450.19791923X-RAY DIFFRACTION98
5.76-7.240.25361450.22871931X-RAY DIFFRACTION98
7.25-56.90.19881500.17291995X-RAY DIFFRACTION95
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)
11.438-0.37250.7231.4159-1.14447.86260.05570.34290.1213-0.172-0.2433-0.1744-0.17670.25250.2280.4225-0.00280.04720.43790.01670.7471-4.516-2.373624.7081
22.13420.5657-0.95792.2422-0.76411.71010.0877-0.1436-0.19170.1762-0.1130.18670.20.029-0.00430.74480.02620.0030.60350.05970.7838-8.6559-40.109359.0551
31.2343-0.6980.13441.34390.19121.13230.04510.0881-0.0162-0.1685-0.0970.12890.1601-0.10620.05750.5154-0.01330.02780.58570.02880.7617-15.9419-19.629635.1052
41.7356-0.93352.08925.8031-0.81025.94770.26690.2205-0.4798-0.4912-0.08730.60390.5666-0.6109-0.21940.5511-0.0242-0.1310.7953-0.1111.043-30.6644-28.952618.6764
54.3661-0.5102-0.69934.98342.45324.3856-0.14390.50620.37120.0219-0.0771-0.1672-1.0116-0.40030.25861.17130.2442-0.0890.88770.16880.8715-19.044518.18130.1645
68.78085.2329-6.54953.1505-3.83134.8549-0.71820.39781.9531-0.04791.1101-0.0004-0.30451.0862-0.58261.0242-0.271-0.02571.17660.01971.0636-9.104113.7093-3.0429
79.5891-2.20931.16585.1345-1.25562.4871-0.05850.46510.90160.14650.14910.4722-1.9365-1.5464-0.08711.69480.3030.0131.00090.20010.8679-19.687220.78025.3264
89.8327-3.7329-3.43382.8517-1.23175.6662-0.38690.8168-1.4158-0.24920.3939-0.06580.3006-0.62510.0041.1604-0.141-0.02431.22610.0061.3627-24.80433.6824-0.1909
94.1886-0.9056-4.3343.6094-1.55296.1882-0.74820.8811-0.3283-0.50320.1090.3347-0.0099-1.58930.40840.84540.0131-0.3011.60750.16390.9588-27.124811.7536-10.2203
102.2880.25780.2465.9658-0.97692.8206-0.8760.67780.97240.47310.54150.7222-0.2079-1.34490.19861.12010.37320.1051.58460.29721.0253-32.081216.7412-4.8728
111.7044-0.7908-3.44232.4677-0.43638.75671.31141.1462-0.2654-0.9439-0.75630.6812-1.2858-0.9391-0.48981.8670.0476-0.45581.720.05921.2365-24.035121.1928-18.3455
128.2839-1.69652.50943.53920.64452.84370.13981.02531.0961-1.2661-0.47970.9563-1.2347-0.00910.43441.84260.1197-0.15111.11990.32691.2317-19.521425.2937-10.047
138.2369-2.7521-0.26559.48360.40296.3504-0.4330.34821.461-1.44570.65971.1181-1.6265-2.0703-0.26311.49710.3673-0.15481.13750.12851.0059-27.659525.93410.1309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 106 through 305 )
2X-RAY DIFFRACTION2chain 'A' and (resid 306 through 503 )
3X-RAY DIFFRACTION3chain 'A' and (resid 504 through 873 )
4X-RAY DIFFRACTION4chain 'A' and (resid 874 through 1051 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 61 )
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 103 )
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 116 )
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 151 )
13X-RAY DIFFRACTION13chain 'B' and (resid 152 through 167 )

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