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- PDB-6ms9: GDP-bound KRAS P34R mutant -

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Basic information

Entry
Database: PDB / ID: 6ms9
TitleGDP-bound KRAS P34R mutant
ComponentsGTPase KRas
KeywordsHYDROLASE / GTPASE KRAS HYDROLYSIS
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 / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / 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:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / RAF activation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / visual learning / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / 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 / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence / DAP12 signaling / 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 nucleotide triphosphate hydrolases ...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 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: 1.49 Å
AuthorsBera, A.K. / Westover, K.D.
CitationJournal: Birth Defects Res / Year: 2020
Title: GTP hydrolysis is modulated by Arg34 in the RASopathy-associated KRASP34R.
Authors: Bera, A.K. / Lu, J. / Lu, C. / Li, L. / Gondi, S. / Yan, W. / Nelson, A. / Zhang, G. / Westover, K.D.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / struct / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,1938
Polymers57,8153
Non-polymers1,3785
Water7,494416
1
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7393
Polymers19,2721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7393
Polymers19,2721
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7152
Polymers19,2721
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.821, 84.397, 88.167
Angle α, β, γ (deg.)90.000, 110.479, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-446-

HOH

21A-395-

HOH

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Components

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


Mass: 19271.760 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.8 M Na/K-phosphate pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 74438 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.9 Å2 / CC1/2: 0.95 / Rpim(I) all: 0.056 / Net I/σ(I): 31
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3609 / CC1/2: 0.827 / Rpim(I) all: 0.242 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3199refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4obe

4obe


Resolution: 1.49→38.69 Å / SU ML: 0.1699 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1861
RfactorNum. reflection% reflection
Rfree0.2323 3785 5.1 %
Rwork0.1949 --
obs0.1968 74231 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.04 Å2
Refinement stepCycle: LAST / Resolution: 1.49→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 58 418 4247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613994
X-RAY DIFFRACTIONf_angle_d0.74165418
X-RAY DIFFRACTIONf_chiral_restr0.06617
X-RAY DIFFRACTIONf_plane_restr0.0046730
X-RAY DIFFRACTIONf_dihedral_angle_d21.94121575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.2829860.2731492X-RAY DIFFRACTION55.52
1.51-1.530.30431340.2662473X-RAY DIFFRACTION94.39
1.53-1.550.27011350.25352655X-RAY DIFFRACTION97.35
1.55-1.570.27591400.25242570X-RAY DIFFRACTION98.3
1.57-1.590.23491220.24252716X-RAY DIFFRACTION99.58
1.59-1.620.27181190.23052643X-RAY DIFFRACTION99.25
1.62-1.640.28031340.23332685X-RAY DIFFRACTION99.4
1.64-1.670.23951320.23322635X-RAY DIFFRACTION99.32
1.67-1.70.26521330.23332656X-RAY DIFFRACTION99.47
1.7-1.740.25391280.21742684X-RAY DIFFRACTION99.22
1.74-1.770.29231570.21372623X-RAY DIFFRACTION99.29
1.77-1.810.25081500.22122649X-RAY DIFFRACTION99.15
1.81-1.850.2281620.22672598X-RAY DIFFRACTION98.5
1.85-1.90.24231410.22652676X-RAY DIFFRACTION99.68
1.9-1.950.28821540.24022636X-RAY DIFFRACTION99.71
1.95-2.010.23861340.20812711X-RAY DIFFRACTION99.68
2.01-2.070.27851440.21232644X-RAY DIFFRACTION99.64
2.07-2.150.22461420.20382643X-RAY DIFFRACTION99.32
2.15-2.230.19371510.19472633X-RAY DIFFRACTION99.39
2.23-2.330.25441590.19952681X-RAY DIFFRACTION99.09
2.33-2.460.2461480.18732661X-RAY DIFFRACTION99.4
2.46-2.610.22221650.18632653X-RAY DIFFRACTION99.93
2.61-2.810.2361560.19092658X-RAY DIFFRACTION99.75
2.81-3.090.19581280.1822679X-RAY DIFFRACTION99.26
3.09-3.540.22251340.16812690X-RAY DIFFRACTION98.91
3.54-4.460.17921350.14272702X-RAY DIFFRACTION99.82
4.46-38.70.21831620.16952700X-RAY DIFFRACTION98.83
Refinement TLS params.Method: refined / Origin x: 31.2934839571 Å / Origin y: 3.95695734406 Å / Origin z: 22.1641614416 Å
111213212223313233
T0.121178697539 Å2-0.0217296209451 Å2-0.015479749584 Å2-0.0565641751724 Å20.038126367914 Å2--0.0887815341406 Å2
L0.439510462533 °2-0.109195141605 °2-0.151385629424 °2-0.190727038219 °20.111461795709 °2--0.280631361523 °2
S0.0169113911003 Å °-0.0425455857728 Å °-0.0321040406956 Å °0.00108599914211 Å °-0.0210880735667 Å °-0.000185847507351 Å °0.0391378258158 Å °-0.0144472838193 Å °-0.00497878939934 Å °
Refinement TLS groupSelection details: all

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