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- PDB-8elv: HRAS R97I Crystal Form 2 -

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Basic information

Entry
Database: PDB / ID: 8elv
TitleHRAS R97I Crystal Form 2
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / Small GTPase Hydrolase HRAS RAS
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / 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 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 / Signaling by FGFR2 in disease / myelination / GRB2 events in EGFR signaling / EPHB-mediated forward 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 / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / RAF activation / Signaling by ERBB2 TMD/JMD mutants / cellular response to gamma radiation / 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 / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / chemotaxis / Regulation of RAS by GAPs / 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 / cellular senescence / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / G protein activity
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 nucleotide triphosphate hydrolases / Rossmann fold ...Small GTPase, Ras-type / Small GTPase Ras domain 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsJohnson, C.W. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1244203 United States
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)21,9075
Polymers21,2801
Non-polymers6274
Water1,31573
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)38.999, 38.999, 158.077
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 21280.111 Da / Num. of mol.: 1 / Mutation: R97I
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-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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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

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: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 8021 / % possible obs: 97.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.032 / Rrim(I) all: 0.095 / Χ2: 0.989 / Net I/σ(I): 7.9 / Num. measured all: 63965
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.20.5283050.6880.3850.6580.46477
2.19-2.232.70.513310.7740.3510.6250.52987.6
2.23-2.273.60.5483980.7770.3160.6370.51795.2
2.27-2.3250.5563850.8190.2690.620.50897.2
2.32-2.3760.5163720.8660.2230.5640.59498.7
2.37-2.427.60.5594310.9040.2120.5990.5399.1
2.42-2.488.90.4493750.940.1580.4770.59398.2
2.48-2.559.70.3883890.9630.1310.410.67898.5
2.55-2.629.80.3724140.9420.1240.3930.74299.3
2.62-2.7110.10.3194000.9730.1040.3360.70199.3
2.71-2.819.90.2564100.9640.0850.270.81599.3
2.81-2.929.90.1963790.9760.0640.2060.89799.2
2.92-3.059.70.1734180.9840.0570.1821.1598.4
3.05-3.219.50.1374130.9840.0460.1451.32599
3.21-3.419.20.1023990.9930.0340.1081.38299.8
3.41-3.689.20.0894140.9920.030.0941.47399.5
3.68-4.058.80.0694190.9930.0240.0731.489100
4.05-4.638.30.0574300.9950.020.061.34499.5
4.63-5.838.60.0534410.9930.0190.0571.30399.3
5.83-508.10.0454980.9970.0170.0481.08199.8

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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: 1CTQ

1ctq


Resolution: 2.153→33.77 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2698 --
Rwork0.1842 --
obs-7480 91.21 %
Displacement parametersBiso max: 76.05 Å2 / Biso mean: 29.8145 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: LAST / Resolution: 2.153→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 35 73 1396

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