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- PDB-5vq2: Crystal structure of human WT-KRAS in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5vq2
TitleCrystal structure of human WT-KRAS in complex with GTP
ComponentsGTPase KRas
KeywordsHYDROLASE
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
GUANOSINE-5'-TRIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsXu, S. / Long, B. / Boris, G. / Ni, S. / Kennedy, M.A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.
Authors: Xu, S. / Long, B.N. / Boris, G.H. / Chen, A. / Ni, S. / Kennedy, M.A.
History
DepositionMay 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)39,8836
Polymers38,7882
Non-polymers1,0954
Water1,928107
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9413
Polymers19,3941
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9413
Polymers19,3941
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.919, 94.919, 120.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A0 - 168
2111B0 - 168

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499791, 0.866146, -0.000222), (0.866146, 0.499791, -0.000608), (-0.000415, -0.000496, -1)0.00667, -0.00535, 0.01126

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Components

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


Mass: 19393.842 Da / Num. of mol.: 2 / Fragment: residues 1-169
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-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, 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 / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 mol/L sodium acetate, 0.1 mol/L Tris pH 8.5, 28% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.96→67.91 Å / Num. obs: 29024 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.169 / Rsym value: 0.14 / Net I/av σ(I): 3.9 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.96-2.0750.7240.90.4010.8990.724100
2.07-2.195.10.5211.30.2890.6540.521100
2.19-2.345.20.3771.30.2060.4690.377100
2.34-2.535.30.2542.90.1350.3120.254100
2.53-2.775.40.18640.0980.2280.186100
2.77-3.15.40.1245.70.0640.1490.124100
3.1-3.585.50.1165.20.0570.1350.116100
3.58-4.385.50.15.90.0490.1150.1100
4.38-6.25.50.0629.50.030.0710.062100
6.2-28.2855.20.04813.40.0250.0570.04893.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→67.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.549 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1514 5.2 %RANDOM
Rwork0.1974 ---
obs0.1991 27523 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.29 Å2 / Biso mean: 32.908 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.29 Å20 Å2
2---0.57 Å20 Å2
3---1.86 Å2
Refinement stepCycle: final / Resolution: 1.96→67.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 66 107 2675
Biso mean--29.8 37.06 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192678
X-RAY DIFFRACTIONr_bond_other_d0.0010.022424
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9773630
X-RAY DIFFRACTIONr_angle_other_deg0.78335624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90624.118136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43815476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.81520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02548
Refine LS restraints NCSNumber: 1282 / Type: TIGHT THERMAL / Rms dev position: 1.45 Å / Weight position: 0.5
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 91 -
Rwork0.305 2073 -
all-2164 -
obs--100 %

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