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- PDB-7f68: Crystal structure of N-ras S89D -

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Basic information

Entry
Database: PDB / ID: 7f68
TitleCrystal structure of N-ras S89D
ComponentsGTPase NRas
KeywordsHYDROLASE / small GTPase / phosphorylation / allosteric / activation / SIGNALING PROTEIN
Function / homology
Function and homology information


myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 ...myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 / 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 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / 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 / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / RAF/MAP kinase cascade / Ras protein signal transduction / Golgi membrane / GTPase activity / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / 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
GUANOSINE-5'-TRIPHOSPHATE / GTPase NRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLi, Y. / Sun, Q.
CitationJournal: To Be Published
Title: Crystal structure of N-ras S89D
Authors: Li, Y. / Sun, Q.
History
DepositionJun 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9154
Polymers19,2721
Non-polymers6443
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-15 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.963, 67.963, 78.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein GTPase NRas / Transforming protein N-Ras


Mass: 19271.865 Da / Num. of mol.: 1 / Mutation: S89D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01111, small monomeric GTPase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion
Details: 0.2 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 23% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 57362 / % possible obs: 97.6 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.042 / Rrim(I) all: 0.164 / Χ2: 1.052 / Net I/σ(I): 5.7 / Num. measured all: 731534
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.24-1.265.21.10323580.370.5011.220.60881.5
1.26-1.2861.01125490.4760.4281.1040.62187.7
1.28-1.316.90.926560.5650.3540.9710.65991.8
1.31-1.348.20.82227440.6980.2960.8760.69894.4
1.34-1.369.90.70328320.8050.230.7410.73297.4
1.36-1.412.50.61728980.8910.1780.6430.81399.7
1.4-1.4313.90.53329090.9310.1440.5520.908100
1.43-1.4713.90.49729120.9220.1350.5151.014100
1.47-1.5113.80.41129100.950.1120.4261.125100
1.51-1.5613.30.36229280.9590.10.3761.199100
1.56-1.6214.20.31629040.9780.0850.3281.183100
1.62-1.6814.60.2929280.9760.0760.31.177100
1.68-1.7614.50.26629170.9750.0710.2751.187100
1.76-1.85140.23729410.9830.0650.2461.125100
1.85-1.9714.80.2229330.9840.0580.2281.15100
1.97-2.1215.30.19329620.9880.050.21.104100
2.12-2.3314.60.1829570.9880.0480.1871.135100
2.33-2.6715.60.16929730.990.0440.1751.122100
2.67-3.3715.30.15430130.9910.0410.161.107100
3.37-5015.10.12731380.9930.0330.1321.15799.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uhv

5uhv


Resolution: 1.24→27.57 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.49 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1443 2966 5.2 %RANDOM
Rwork0.1226 ---
obs0.1237 54360 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.51 Å2 / Biso mean: 24.178 Å2 / Biso min: 13.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: final / Resolution: 1.24→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 38 226 1614
Biso mean--20.59 42.41 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131499
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171374
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6542045
X-RAY DIFFRACTIONr_angle_other_deg1.5211.5853193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03422.04883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8991512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
X-RAY DIFFRACTIONr_rigid_bond_restr2.67532873
LS refinement shellResolution: 1.244→1.276 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 157 -
Rwork0.311 3030 -
all-3187 -
obs--73.16 %

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