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- PDB-4q01: Second-site screening of K-Ras in the presence of covalently atta... -

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Basic information

Entry
Database: PDB / ID: 4q01
TitleSecond-site screening of K-Ras in the presence of covalently attached first-site ligands
ComponentsK-RasKRAS
KeywordsHYDROLASE / small GTPase / signaling transduction / Sos / Raf / cytosol
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / 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 / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / 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 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / 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 / cytoplasmic side of plasma membrane / Signaling by SCF-KIT / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
naphthalene-1-thiol / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.291 Å
AuthorsSun, Q. / Phan, J. / Friberg, A. / Camper, D.V. / Olejniczak, E.T. / Fesik, S.W.
CitationJournal: J.Biomol.Nmr / Year: 2014
Title: A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand.
Authors: Sun, Q. / Phan, J. / Friberg, A.R. / Camper, D.V. / Olejniczak, E.T. / Fesik, S.W.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K-Ras
B: K-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8838
Polymers38,6282
Non-polymers1,2556
Water7,819434
1
A: K-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9424
Polymers19,3141
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: K-Ras
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9424
Polymers19,3141
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.314, 83.671, 104.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein K-Ras / KRAS


Mass: 19313.838 Da / Num. of mol.: 2 / Mutation: G12V, S39C, C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-2XH / naphthalene-1-thiol / 1-Naphthalenethiol


Mass: 160.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 39.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 4000, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.29→25.01 Å / Num. all: 79531 / Num. obs: 79519 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.29→1.34 Å / % possible all: 93.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.291→25.01 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 3980 5.01 %
Rwork0.1881 --
obs0.1893 79519 97.98 %
all-79531 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.291→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 80 434 3193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122807
X-RAY DIFFRACTIONf_angle_d1.4683802
X-RAY DIFFRACTIONf_dihedral_angle_d15.5781051
X-RAY DIFFRACTIONf_chiral_restr0.078423
X-RAY DIFFRACTIONf_plane_restr0.007482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2907-1.30640.30211250.27492472X-RAY DIFFRACTION92
1.3064-1.32290.30871210.29372601X-RAY DIFFRACTION96
1.3229-1.34040.2911410.26692668X-RAY DIFFRACTION96
1.3404-1.35870.28061550.25732603X-RAY DIFFRACTION97
1.3587-1.37810.30311330.25672651X-RAY DIFFRACTION99
1.3781-1.39870.28211400.24062710X-RAY DIFFRACTION98
1.3987-1.42050.28121460.24032696X-RAY DIFFRACTION99
1.4205-1.44380.26891360.23072730X-RAY DIFFRACTION100
1.4438-1.46870.21581370.22382672X-RAY DIFFRACTION99
1.4687-1.49540.26091450.22212743X-RAY DIFFRACTION100
1.4954-1.52420.24741390.21422707X-RAY DIFFRACTION99
1.5242-1.55530.22651330.2092702X-RAY DIFFRACTION100
1.5553-1.58910.24591550.20082715X-RAY DIFFRACTION99
1.5891-1.62610.22941310.20142727X-RAY DIFFRACTION100
1.6261-1.66670.23191530.20052714X-RAY DIFFRACTION100
1.6667-1.71180.24841460.1882742X-RAY DIFFRACTION100
1.7118-1.76210.231410.19212744X-RAY DIFFRACTION100
1.7621-1.8190.21331500.1932773X-RAY DIFFRACTION100
1.819-1.8840.23831340.19782725X-RAY DIFFRACTION100
1.884-1.95940.21561480.19232709X-RAY DIFFRACTION99
1.9594-2.04850.20871390.18542759X-RAY DIFFRACTION100
2.0485-2.15650.22811630.18122753X-RAY DIFFRACTION100
2.1565-2.29150.20341420.17992761X-RAY DIFFRACTION99
2.2915-2.46830.20711580.17562781X-RAY DIFFRACTION100
2.4683-2.71640.18691690.17742766X-RAY DIFFRACTION100
2.7164-3.10880.19341330.17842829X-RAY DIFFRACTION100
3.1088-3.91440.17361140.16462363X-RAY DIFFRACTION88
3.9144-25.01520.19511530.16692723X-RAY DIFFRACTION92

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