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- PDB-8elu: HRAS R97G Crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 8elu
TitleHRAS R97G Crystal form 1
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / Small GTPase / Hydrolase / HRAS / RAS
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / 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 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / 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 / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / 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 / intrinsic apoptotic signaling pathway / small monomeric GTPase / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / positive regulation of MAP kinase activity / 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 / cellular response to gamma radiation / Regulation of RAS by GAPs / endocytosis / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / insulin receptor signaling pathway
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsJohnson, C.W. / Rodrigues, J.A. / Mattos, C.
Funding support1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1244203
CitationJournal: Protein Sci. / Year: 2023
Title: Allosteric site variants affect GTP hydrolysis on Ras.
Authors: Johnson, C.W. / Fetics, S.K. / Davis, K.P. / Rodrigues, J.A. / Mattos, C.
History
DepositionSep 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8355
Polymers21,2241
Non-polymers6114
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.636, 88.636, 135.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-203-

MG

21A-334-

HOH

31A-411-

HOH

41A-440-

HOH

51A-442-

HOH

61A-443-

HOH

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Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 21224.004 Da / Num. of mol.: 1 / Mutation: R97G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01112, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Calcium Acetate, Magnesium Chloride, Sodium Chloride, DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 15658 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Χ2: 0.918 / Net I/σ(I): 9.5 / Num. measured all: 166943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9610.50.8427880.890.2730.8850.802100
1.96-210.60.5467680.9290.1760.5730.57100
2-2.0410.60.4547580.9380.1460.4770.646100
2.04-2.0810.10.6367780.8960.2120.671.769100
2.08-2.1210.60.4287720.960.1380.450.839100
2.12-2.1710.70.2757630.9760.0880.2890.656100
2.17-2.2310.70.2947870.9790.0940.3090.736100
2.23-2.2910.10.3627730.9570.1210.3821.897100
2.29-2.3610.80.1777780.9910.0560.1860.606100
2.36-2.4310.80.1457700.9930.0460.1520.594100
2.43-2.5210.80.1297760.9960.0410.1360.637100
2.52-2.6210.80.1117780.9970.0350.1160.681100
2.62-2.7410.80.1377880.9940.0440.1441.083100
2.74-2.8810.90.087740.9980.0250.0840.691100
2.88-3.0610.90.0667830.9970.0210.0690.721100
3.06-3.310.90.0477870.9990.0150.0490.691100
3.3-3.6310.80.0497820.9990.0160.0511.189100
3.63-4.1610.70.0448010.9990.0140.0461.521100
4.16-5.2410.80.02781410.0090.0291.059100
5.24-5010.30.02884010.0090.0291.05299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8Y

3k8y


Resolution: 1.93→36.9 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.209 --
Rwork0.177 --
obs-15658 99.7 %
Displacement parametersBiso max: 73.35 Å2 / Biso mean: 31.5248 Å2 / Biso min: 13.48 Å2
Refinement stepCycle: LAST / Resolution: 1.93→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 35 143 1449

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