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- PDB-6bof: Crystal structure of KRAS A146T-GDP demonstrating open switch 1 c... -

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Basic information

Entry
Database: PDB / ID: 6bof
TitleCrystal structure of KRAS A146T-GDP demonstrating open switch 1 conformation
ComponentsGTPase KRas
KeywordsHYDROLASE / small gtpase / signal transduction / GDP binding
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 nucleotide triphosphate hydrolases ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsBera, A.K. / Yan, W. / Westover, K.D.
CitationJournal: Cancer Discov / Year: 2019
Title: Tissue-Specific Oncogenic Activity of KRASA146T.
Authors: Poulin, E.J. / Bera, A.K. / Lu, J. / Lin, Y.J. / Strasser, S.D. / Paulo, J.A. / Huang, T.Q. / Morales, C. / Yan, W. / Cook, J. / Nowak, J.A. / Brubaker, D.K. / Joughin, B.A. / Johnson, C.W. ...Authors: Poulin, E.J. / Bera, A.K. / Lu, J. / Lin, Y.J. / Strasser, S.D. / Paulo, J.A. / Huang, T.Q. / Morales, C. / Yan, W. / Cook, J. / Nowak, J.A. / Brubaker, D.K. / Joughin, B.A. / Johnson, C.W. / DeStefanis, R.A. / Ghazi, P.C. / Gondi, S. / Wales, T.E. / Iacob, R.E. / Bogdanova, L. / Gierut, J.J. / Li, Y. / Engen, J.R. / Perez-Mancera, P.A. / Braun, B.S. / Gygi, S.P. / Lauffenburger, D.A. / Westover, K.D. / Haigis, K.M.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2284
Polymers38,3412
Non-polymers8862
Water5,963331
1
A: GTPase KRas
hetero molecules

B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2284
Polymers38,3412
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3060 Å2
ΔGint-19 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.024, 78.024, 55.863
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-456-

HOH

31A-462-

HOH

41B-450-

HOH

51B-459-

HOH

61B-465-

HOH

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Components

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


Mass: 19170.588 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / References: UniProt: P01116
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M sodium malonate, pH 7.0, 0.1 M Bis-Tris propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 74694 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.09
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.71 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_2932refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4OBE

4obe


Resolution: 1.401→28.909 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 12.78
RfactorNum. reflection% reflection
Rfree0.1449 3663 4.91 %
Rwork0.1116 --
obs0.1132 74666 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.8 Å2 / Biso mean: 24.829 Å2 / Biso min: 10.15 Å2
Refinement stepCycle: final / Resolution: 1.401→28.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 85 331 3104
Biso mean--20.1 40.16 -
Num. residues----336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4009-1.41930.21121330.175327392872100
1.4193-1.43880.21461140.1682701281599
1.4388-1.45930.22411490.148327432892100
1.4593-1.48110.19871440.14692728287299
1.4811-1.50430.2061640.1427292893100
1.5043-1.52890.18651120.124427802892100
1.5289-1.55530.17921560.112726802836100
1.5553-1.58360.14761490.101927252874100
1.5836-1.6140.13371400.100827072847100
1.614-1.6470.15211530.095827342887100
1.647-1.68280.14611280.098527722900100
1.6828-1.72190.14081400.098826812821100
1.7219-1.7650.13061240.095727702894100
1.765-1.81270.16221740.088827362910100
1.8127-1.8660.13391490.091627102859100
1.866-1.92620.12191420.091427652907100
1.9262-1.99510.14871030.088927292832100
1.9951-2.07490.14161220.096727492871100
2.0749-2.16930.12521520.099627262878100
2.1693-2.28370.1231840.094227082892100
2.2837-2.42670.12881150.097727382853100
2.4267-2.61390.13441580.109127202878100
2.6139-2.87670.15441820.114226942876100
2.8767-3.29250.14011300.120927432873100
3.2925-4.14630.14851530.105527212874100
4.1463-28.91560.1479930.1432775286899

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