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- PDB-9o0s: Crystal structure of KRAS-Q61R mutant, GMPPNP-bound -

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Basic information

Entry
Database: PDB / ID: 9o0s
TitleCrystal structure of KRAS-Q61R mutant, GMPPNP-bound
ComponentsGTPase KRas
KeywordsONCOPROTEIN / KRAS / RAS / K-ras / KRAS4b / Q61R
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / positive regulation of glial cell proliferation / Tie2 Signaling / FRS-mediated FGFR1 signaling / homeostasis of number of cells within a tissue / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity / actin cytoskeleton organization / Ca2+ pathway / RAF/MAP kinase cascade / neuron apoptotic process / gene expression / negative regulation of neuron apoptotic process / mitochondrial outer membrane / Ras protein signal transduction / Golgi membrane / focal adhesion / GTPase activity
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsChan, A.H. / Davies, D. / Abendroth, J. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Biophysical and structural analysis of KRAS switch-II pocket inhibitors reveals allele-specific binding constraints.
Authors: Alexander, P. / Chan, A.H. / Rabara, D. / Swain, M. / Larsen, E.K. / Dyba, M. / Chertov, O. / Ashraf, M. / Champagne, A. / Lin, K. / Maciag, A. / Gillette, W.K. / Nissley, D.V. / McCormick, ...Authors: Alexander, P. / Chan, A.H. / Rabara, D. / Swain, M. / Larsen, E.K. / Dyba, M. / Chertov, O. / Ashraf, M. / Champagne, A. / Lin, K. / Maciag, A. / Gillette, W.K. / Nissley, D.V. / McCormick, F. / Simanshu, D.K. / Stephen, A.G.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9043
Polymers19,3581
Non-polymers5472
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.750, 69.750, 92.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

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Components

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19357.875 Da / Num. of mol.: 1 / Mutation: Q61R
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, small monomeric GTPase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 8000, 20% PEG 400, 100 mM magnesium chloride, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.89→36.78 Å / Num. obs: 12780 / % possible obs: 94.4 % / Redundancy: 4 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.084 / Net I/σ(I): 11.78
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 904 / CC1/2: 0.563 / Rrim(I) all: 0.808 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJun 30, 2024 BUILT=20241002data reduction
XSCALEJun 30, 2024 BUILT=20241002data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→36.78 Å / SU ML: 0.2797 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.7284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1266 9.91 %
Rwork0.1975 11512 -
obs0.2009 12778 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.52 Å2
Refinement stepCycle: LAST / Resolution: 1.89→36.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 33 50 1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661371
X-RAY DIFFRACTIONf_angle_d0.84631863
X-RAY DIFFRACTIONf_chiral_restr0.0507211
X-RAY DIFFRACTIONf_plane_restr0.0068236
X-RAY DIFFRACTIONf_dihedral_angle_d13.6788527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.960.41541300.33351250X-RAY DIFFRACTION92.62
1.96-2.050.31881450.28651327X-RAY DIFFRACTION96.71
2.05-2.160.29331410.26281283X-RAY DIFFRACTION96.22
2.16-2.290.28211480.24251306X-RAY DIFFRACTION96.29
2.29-2.470.27941310.22991315X-RAY DIFFRACTION95.45
2.47-2.720.28671350.21741281X-RAY DIFFRACTION94.84
2.72-3.110.24761310.19971276X-RAY DIFFRACTION94.24
3.11-3.920.19171460.1691269X-RAY DIFFRACTION92.79
3.92-36.780.16491590.14351205X-RAY DIFFRACTION90.51
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)
10.8253653545980.4712292402970.2587318308753.249907159130.401793409790.105260103675-0.0541033534839-0.1887087261480.303735430466-0.351989648393-0.2448973594871.10783775765-0.209015789723-0.3201653885430.04699394321840.2818997932640.0289027617419-0.1323464931890.39102861459-0.1384757944030.398283163566-30.56332385591.49806158561-16.6663583686
21.43989059944-0.1758478350980.4295497406490.64294120350.8825346043191.88484196678-0.1116030786750.242984092451-0.516034197402-0.397324671365-0.02126236072680.695154387438-0.0010911093405-0.315746865835-0.07932564789720.168463179459-0.0646580927878-0.08903121393220.257035096878-0.05053592119610.465573962679-23.1572451201-4.32022520925-19.8469304742
30.5851014666240.182203335876-0.1546820773350.5409549574770.2465095811080.625901978337-0.00608008258082-0.267185676220.545747785429-0.1006352579690.004232397133310.364304907846-0.211328779270.0796887393193-0.005578300512220.218832665758-0.006404510424550.00156792659890.167424513973-0.01454853062060.294064591863-16.02019478876.17576412178-13.2340175008
40.480696973599-0.0774695095415-0.1968595272480.6683833889480.4540358011931.189374504940.0496970143004-0.717421995904-0.0912415827228-0.006270433280340.03492031071650.6130800442160.1414127525320.03448767704340.1375435798650.1098713625310.005795192121560.0795577057090.315318536339-0.01420376847310.372016740228-19.925691824-0.842992518126-5.36429678293
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )1 - 101 - 10
22chain 'A' and (resid 11 through 74 )11 - 7411 - 74
33chain 'A' and (resid 75 through 116 )75 - 11675 - 116
44chain 'A' and (resid 117 through 168 )117 - 168117 - 168

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