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- PDB-9u90: Crystal structure of KRAS-G12D/E62K mutant in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 9u90
TitleCrystal structure of KRAS-G12D/E62K mutant in complex with GDP
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / Complex structure
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / myoblast proliferation / 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 / positive regulation of glial cell proliferation / skeletal muscle cell differentiation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / cardiac muscle cell proliferation / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / glial cell proliferation / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / striated muscle cell differentiation / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / response to glucocorticoid / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Ras activation upon Ca2+ influx through NMDA receptor / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / female pregnancy / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / RAF activation / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / visual learning / regulation of long-term neuronal synaptic plasticity / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Negative regulation of MAPK pathway / Regulation of RAS by GAPs / RAS processing / positive regulation of cellular senescence / Signaling by BRAF and RAF1 fusions / DAP12 signaling / GDP binding / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsZhang, X.L. / Zhang, X.Y. / Zhang, Y.Z. / Xu, C. / Liu, L. / Bai, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other government24JS2850100 China
CitationJournal: To Be Published
Title: Molecule Mechanisms of KRAS Secondery Mutation Conferred Resistance of MRTX1133
Authors: Zhang, X.L. / Zhang, X.Y. / Zhang, Y.Z. / Bai, F.
History
DepositionMar 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0964
Polymers21,6041
Non-polymers4923
Water2,522140
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)41.226, 51.682, 67.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2B of GTPase KRas / GTPase KRAS / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21604.260 Da / Num. of mol.: 1 / Mutation: G12D,E62K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.67 Å3/Da / Density % sol: 26.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG buffer pH 7.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 46007 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Χ2: 1.026 / Net I/σ(I): 6.4 / Num. measured all: 555895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.2-1.226.90.35822300.9280.9810.1450.3870.73499.7
1.22-1.248.50.36822690.9360.9830.1310.3910.858100
1.24-1.2710.80.3922570.9340.9830.1230.411.098100
1.27-1.2912.30.36322880.9520.9880.1050.3781.128100
1.29-1.3212.90.34422630.960.990.0970.3581.235100
1.32-1.3512.80.32622960.9660.9910.0930.3391.284100
1.35-1.3912.20.30622570.970.9920.0890.3191.289100
1.39-1.4212.60.28222680.9710.9930.0810.2941.26100
1.42-1.4612.60.26122810.9660.9910.0760.2721.349100
1.46-1.5113.10.23522630.9770.9940.0660.2451.333100
1.51-1.5712.90.21722970.9790.9950.0620.2261.345100
1.57-1.6312.30.19722890.9840.9960.0580.2051.251100
1.63-1.712.60.18122900.9810.9950.0530.1881.15100
1.7-1.79130.15923190.990.9970.0450.1651.021100
1.79-1.913.20.14122860.9910.9980.040.1460.927100
1.9-2.0512.60.12823130.9930.9980.0370.1340.85100
2.05-2.2612.80.11323200.9940.9990.0330.1180.737100
2.26-2.5913.20.09623540.9960.9990.0270.10.579100
2.59-3.2612.30.07523630.9970.9990.0220.0780.44100
3.26-5011.90.07225040.9930.9980.0220.0750.517100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→33.81 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 2305 5.06 %
Rwork0.1715 --
obs0.173 45586 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 30 140 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071415
X-RAY DIFFRACTIONf_angle_d1.0611917
X-RAY DIFFRACTIONf_dihedral_angle_d27.971201
X-RAY DIFFRACTIONf_chiral_restr0.084214
X-RAY DIFFRACTIONf_plane_restr0.005245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.26291420.23052425X-RAY DIFFRACTION91
1.23-1.250.24371350.20022609X-RAY DIFFRACTION97
1.25-1.290.23441420.1842661X-RAY DIFFRACTION99
1.29-1.320.19781330.18542698X-RAY DIFFRACTION100
1.32-1.360.21991510.18312671X-RAY DIFFRACTION100
1.36-1.40.24681480.17922701X-RAY DIFFRACTION100
1.4-1.450.21661420.17872701X-RAY DIFFRACTION100
1.45-1.510.21411310.16822709X-RAY DIFFRACTION100
1.51-1.580.19011560.16032730X-RAY DIFFRACTION100
1.58-1.660.17981420.16472714X-RAY DIFFRACTION100
1.66-1.770.19781400.16832722X-RAY DIFFRACTION100
1.77-1.90.211510.16432723X-RAY DIFFRACTION100
1.9-2.10.20741450.15642737X-RAY DIFFRACTION100
2.1-2.40.18171530.16472756X-RAY DIFFRACTION100
2.4-3.020.21031490.18162792X-RAY DIFFRACTION100
3.02-33.810.19741450.17172932X-RAY DIFFRACTION100

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