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- PDB-8eer: KRAS4B A146V 1-185 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8eer
TitleKRAS4B A146V 1-185 bound to GDP
ComponentsIsoform 4b of the GTPase KRAS
KeywordsONCOPROTEIN / small GTPase / mutant KRas
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / G protein activity / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / MAPK cascade / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / negative regulation of neuron apoptotic process / Ras protein signal transduction / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family 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: 1.18 Å
AuthorsBetts, L. / Rossman, K.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA223495 United States
CitationJournal: To Be Published
Title: KRAS4B A146V 1-185 bound to GDP
Authors: Rossman, K.L. / Betts, L.
History
DepositionSep 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 4b of the GTPase KRAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5712
Polymers21,1281
Non-polymers4431
Water3,477193
1
A: Isoform 4b of the GTPase KRAS
hetero molecules

A: Isoform 4b of the GTPase KRAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1434
Polymers42,2562
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_768-x+2,-x+y+1,-z+31
Buried area3220 Å2
ΔGint-20 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.181, 78.181, 55.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-488-

HOH

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Components

#1: Protein Isoform 4b of the GTPase KRAS / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21128.107 Da / Num. of mol.: 1 / Mutation: A146V
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.14 % / Description: hexagonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 22% PEG3350, 200 mM lithium citrate, 10 mM Tris-HCl pH 8, 20 mM NaCl, 2 mM DTT, 1 mM magnesium chloride, 10 uM GDP, 12.8 mg/mL KRAS4B A146V

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97817 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97817 Å / Relative weight: 1
ReflectionResolution: 1.18→55.77 Å / Num. obs: 63328 / % possible obs: 99.29 % / Redundancy: 10.3 % / Biso Wilson estimate: 11.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07678 / Rpim(I) all: 0.02466 / Rrim(I) all: 0.08072 / Net I/σ(I): 15.72
Reflection shellResolution: 1.184→1.227 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 5910 / CC1/2: 0.7561 / Rpim(I) all: 0.3211 / Rrim(I) all: 0.8649 / % possible all: 93.06

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBE

4obe


Resolution: 1.18→55.77 Å / SU ML: 0.1266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1718 1995 3.15 %
Rwork0.1541 61313 -
obs0.1547 63308 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.07 Å2
Refinement stepCycle: LAST / Resolution: 1.18→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 0 193 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081426
X-RAY DIFFRACTIONf_angle_d1.12411938
X-RAY DIFFRACTIONf_chiral_restr0.0728217
X-RAY DIFFRACTIONf_plane_restr0.0094249
X-RAY DIFFRACTIONf_dihedral_angle_d16.3717546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.32841160.3173451X-RAY DIFFRACTION77.49
1.21-1.240.26681440.22274347X-RAY DIFFRACTION97.4
1.24-1.280.16251420.16844337X-RAY DIFFRACTION97.86
1.28-1.320.16461450.15294363X-RAY DIFFRACTION97.89
1.32-1.370.16441410.14574374X-RAY DIFFRACTION98.24
1.37-1.420.15791440.1454411X-RAY DIFFRACTION98.57
1.42-1.490.17991450.16184411X-RAY DIFFRACTION98.79
1.49-1.560.15451410.14484425X-RAY DIFFRACTION98.96
1.56-1.660.17751460.13374456X-RAY DIFFRACTION99.29
1.66-1.790.16221400.13194466X-RAY DIFFRACTION99.59
1.79-1.970.15721460.14524489X-RAY DIFFRACTION99.63
1.97-2.260.1461450.1394515X-RAY DIFFRACTION99.87
2.26-2.840.16971440.1544561X-RAY DIFFRACTION100
2.84-55.770.17991560.15984707X-RAY DIFFRACTION99.94

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