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- PDB-7kyz: Solution structures of full-length K-RAS bound to GDP -

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Basic information

Entry
Database: PDB / ID: 7kyz
TitleSolution structures of full-length K-RAS bound to GDP
ComponentsIsoform 2B of GTPase KRas
KeywordsCELL CYCLE
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / 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 / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / 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 / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / positive regulation of glial cell proliferation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 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 / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by CSF1 (M-CSF) in myeloid cells / 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 / mitochondrial outer membrane / negative regulation of neuron apoptotic process / Ras protein signal transduction / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSharma, A.K. / Maciag, A.E.
CitationJournal: To Be Published
Title: Solution structures of full-length K-RAS bound to GDP
Authors: Sharma, A.K. / Maciag, A.E.
History
DepositionDec 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas


Theoretical massNumber of molelcules
Total (without water)21,4601
Polymers21,4601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

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


Mass: 21459.605 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, small monomeric GTPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic31D 1H
122isotropic32D 1H-15N HSQC
133isotropic12D 1H-13C HSQC aliphatic
143isotropic12D 1H-13C HSQC aromatic
152isotropic33D 1H-15N TOCSY
1153isotropic33D HN(CA)CB
1143isotropic33D CBCA(CO)NH
1133isotropic33D HNCA
1123isotropic33D HN(CO)CA
1113isotropic33D C(CO)NH
1103isotropic33D HNCO
193isotropic23D 1H-15N NOESY
183isotropic22D 1H-13C HSQC aromatic
173isotropic23D 1H-13C NOESY aliphatic
163isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution20.7-0.9 mM [U-100% 15N] GTPase KRas, 20 mM [U-2H] MES, 100 mM potassium chloride, 50 mM sodium chloride, 2 mM MgCl2, 1 mM [U-2H] TCEP, 7 mM [U-2H] D2O, 0.05 % sodium azide, 90% H2O/10% D2O0.7-0.9 mM sample was treated with 2.5% of DMSO to match equal composition of a separate sample that was treated with small-molecule cysteine inhibitor in DMSO. Sample was subsequently purified using Liquid Chromatography (FPLC) system.15N_sample90% H2O/10% D2O
solution30.7-0.9 mM [U-13C; U-15N] GTPase KRas, 20 mM [U-2H] MES, 100 mM potassium chloride, 50 mM sodium chloride, 2 mM MgCl2, 1 mM [U-2H] TCEP, 7 mM [U-2H] D2O, 0.05 % sodium azide, 90% H2O/10% D2O0.7-0.9 mM sample was treated with 2.5% of DMSO to match equal composition of a separate sample that was treated with small-molecule cysteine inhibitor in DMSO. Sample was subsequently purified using Liquid Chromatography (FPLC) system.13C15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMMES[U-2H]2
100 mMpotassium chloridenatural abundance2
50 mMsodium chloridenatural abundance2
2 mMMgCl2natural abundance2
1 mMTCEP[U-2H]2
7 mMD2O[U-2H]2
0.05 %sodium azidenatural abundance2
20 mMMES[U-2H]3
100 mMpotassium chloridenatural abundance3
50 mMsodium chloridenatural abundance3
2 mMMgCl2natural abundance3
1 mMTCEP[U-2H]3
7 mMD2O[U-2H]3
0.05 %sodium azidenatural abundance3
mMGTPase KRas[U-13C; U-15N]0.7-0.93
mMGTPase KRas[U-100% 15N]0.7-0.92
Sample conditionsDetails: Samples were freshly prepared in NMR buffer pH 6.5. NMR Data was collected with 320 uL sample volume at 298K. Sample apparently held the concentration during the week long data acquisition ...Details: Samples were freshly prepared in NMR buffer pH 6.5. NMR Data was collected with 320 uL sample volume at 298K. Sample apparently held the concentration during the week long data acquisition with one sample. Two 13C15N labeled NMR samples and one 15N labeled NMR sample was used for all data collection.
Ionic strength: 0.15 M / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD8001TS 3.5.6
Bruker AVANCEBrukerAVANCE9002TS 2.1.6
Bruker AVANCE IIIBrukerAVANCE III7003TS 3.5.6

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospincollection
NMRPipe10.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
PONDEROSALee W, Petit CM, Cornilescu G, Stark JL, Markley JL.peak picking
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
PONDEROSALee W, Petit CM, Cornilescu G, Stark JL, Markley JL.refinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4
Details: structures are based on 2140 distance restraints, 138 hydrogen bond restraints as deduced from secondary structure and the tertiary fold detremined using refinement process, and 238 dihedral angle restraints
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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