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- PDB-6e6f: KRAS G13D bound to GppNHp (K13GNP) -

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Basic information

Entry
Database: PDB / ID: 6e6f
TitleKRAS G13D bound to GppNHp (K13GNP)
ComponentsGTPase KRas
KeywordsSIGNALING PROTEIN / Oncogene / RAS / p21
Function / homology
Function and homology information


endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / positive regulation of Rac protein signal transduction / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation ...endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / positive regulation of Rac protein signal transduction / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / Signaling by RAS GTPase mutants / Signaling by RAS GAP mutants / Activation of RAS in B cells / RUNX3 regulates p14-ARF / RAS signaling downstream of NF1 loss-of-function variants / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Estrogen-stimulated signaling through PRKCZ / homeostasis of number of cells within a tissue / Signaling by PDGFRA extracellular domain mutants / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / SHC-mediated cascade:FGFR3 / Signaling by FGFR4 in disease / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR4 / Signaling by FLT3 ITD and TKD mutants / SHC-mediated cascade:FGFR1 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Tie2 Signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / G protein activity / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in EGFR signaling / p38MAPK events / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / small monomeric GTPase / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / NCAM signaling for neurite out-growth / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / visual learning / regulation of long-term neuronal synaptic plasticity / RAF activation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Ca2+ pathway / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / extrinsic component of cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / GDP binding / Negative regulation of MAPK pathway / regulation of protein stability / RAS processing / Signaling by RAF1 mutants / actin cytoskeleton organization / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by moderate kinase activity BRAF mutants / Signaling by BRAF and RAF1 fusions / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ras protein signal transduction / neuron apoptotic process / RAF/MAP kinase cascade / mitochondrial outer membrane / negative regulation of neuron apoptotic process / GTPase activity / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.401 Å
AuthorsJohnson, C.W. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517295 United States
CitationJournal: Cell Rep / Year: 2019
Title: Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D.
Authors: Johnson, C.W. / Lin, Y.J. / Reid, D. / Parker, J. / Pavlopoulos, S. / Dischinger, P. / Graveel, C. / Aguirre, A.J. / Steensma, M. / Haigis, K.M. / Mattos, C.
History
DepositionJul 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_related / refine / reflns
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _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 / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.pdbx_method_to_determine_struct / _reflns.number_all / _reflns.number_obs / _reflns.percent_possible_obs
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,9535
Polymers37,8852
Non-polymers1,0693
Water1448
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4893
Polymers18,9421
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4652
Polymers18,9421
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.486, 39.096, 89.319
Angle α, β, γ (deg.)90.000, 124.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18942.320 Da / Num. of mol.: 2 / Fragment: residues 1-166 / Mutation: G13D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET21 / Details (production host): ampicillin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01116
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
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 / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5 mM Sodium acetate, 91 mM sodium citrate tribasic, 183 mM Ammonium acetate, 27.2% PEG 4000, 4.3% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, at pH 7.5), crystals grown 1uL ...Details: 5 mM Sodium acetate, 91 mM sodium citrate tribasic, 183 mM Ammonium acetate, 27.2% PEG 4000, 4.3% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, at pH 7.5), crystals grown 1uL by 1uL mother liquor to protein (22mg/mL), No cryoprotectant was used for diffraction

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Data collection

DiffractionMean temperature: 173.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 22660 / Num. obs: 4526 / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.31 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.074 / Rrim(I) all: 0.16 / Χ2: 0.929 / Net I/σ(I): 6.6 / Num. measured all: 22660
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.051.60.4121630.7320.3480.5421.06846
3.05-3.111.90.371830.7940.2930.4750.88859.4
3.11-3.171.90.3982380.8110.3080.5070.85767.4
3.17-3.232.10.3062590.8750.220.380.98974.9
3.23-3.32.40.2672870.8990.1830.3270.76484.4
3.3-3.382.80.3323000.9140.210.3960.94791.7
3.38-3.4630.2843230.8910.1690.3331.04495.8
3.46-3.563.30.2693370.9420.1520.3110.96595.5
3.56-3.663.60.2373250.9510.1330.2740.9196.4
3.66-3.7840.2363340.9590.1220.2671.09898.2
3.78-3.913.90.23480.9620.1070.2280.94196.9
3.91-4.074.50.1753250.9690.0870.1960.98797
4.07-4.264.20.1383350.9840.0710.1560.90697.7
4.26-4.484.40.1323340.980.0670.1491.06197.9
4.48-4.764.50.1193390.9870.0580.1330.91197.7
4.76-5.134.60.1213420.9850.0590.1350.86397.4
5.13-5.644.50.1273240.9870.0620.1420.79596.4
5.64-6.464.60.1393450.980.0660.1540.88996.6
6.46-8.134.50.0913420.9930.0440.1010.7996.9
8.13-504.30.0673620.9860.0330.0750.97495.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→36.1 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.63
RfactorNum. reflection% reflection
Rfree0.258 453 9.83 %
Rwork0.182 --
obs0.187 4524 80.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.48 Å2 / Biso mean: 40.4599 Å2 / Biso min: 13.07 Å2
Refinement stepCycle: final / Resolution: 3.401→47.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 65 8 2281
Biso mean--41.16 31.97 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112313
X-RAY DIFFRACTIONf_angle_d1.3753167
X-RAY DIFFRACTIONf_chiral_restr0.071380
X-RAY DIFFRACTIONf_plane_restr0.007402
X-RAY DIFFRACTIONf_dihedral_angle_d19.2941361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4008-3.66320.25971080.1861944105260
3.6632-4.03170.27581290.16621160128972
4.0317-4.61470.20391490.1521358150787
4.6147-5.81230.27731560.18831453160992
5.8123-47.2540.26261540.19831472162692

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