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- PDB-7jii: HRAS A59E GDP -

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Basic information

Entry
Database: PDB / ID: 7jii
TitleHRAS A59E GDP
ComponentsGTPase HRasHRAS
KeywordsONCOPROTEIN / Mutant Cancer GTPase
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 / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / 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 / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / 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 / positive regulation of protein targeting to membrane / 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 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / 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 / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / 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 / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / cellular response to gamma radiation / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / 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 / chemotaxis / positive regulation of fibroblast proliferation / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling
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'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.532 Å
AuthorsJohnson, C.W. / Haigis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA230718 United States
American Cancer Society30428-PF-17-066-01-TBG United States
CitationJournal: Mol.Cell / Year: 2022
Title: Regulation of GTPase function by autophosphorylation.
Authors: Johnson, C.W. / Seo, H.S. / Terrell, E.M. / Yang, M.H. / KleinJan, F. / Gebregiworgis, T. / Gasmi-Seabrook, G.M.C. / Geffken, E.A. / Lakhani, J. / Song, K. / Bashyal, P. / Popow, O. / Paulo, ...Authors: Johnson, C.W. / Seo, H.S. / Terrell, E.M. / Yang, M.H. / KleinJan, F. / Gebregiworgis, T. / Gasmi-Seabrook, G.M.C. / Geffken, E.A. / Lakhani, J. / Song, K. / Bashyal, P. / Popow, O. / Paulo, J.A. / Liu, A. / Mattos, C. / Marshall, C.B. / Ikura, M. / Morrison, D.K. / Dhe-Paganon, S. / Haigis, K.M.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,96210
Polymers37,8662
Non-polymers1,0958
Water6,053336
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4815
Polymers18,9331
Non-polymers5484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4815
Polymers18,9331
Non-polymers5484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.593, 37.946, 56.254
Angle α, β, γ (deg.)107.360, 107.190, 95.320
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18933.227 Da / Num. of mol.: 2 / Mutation: A59E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P01112
#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 / Feature type: SUBJECT OF INVESTIGATION / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Starting concentration of HRAS A59T GppNHp was 15.2mg/mL in buffer containing 20mM HEPES, 50mM NaCl, 20mM MgCl2 and 1mM DTT at pH 7.5. Used a 24-well plate sealed with Vaseline and total ...Details: Starting concentration of HRAS A59T GppNHp was 15.2mg/mL in buffer containing 20mM HEPES, 50mM NaCl, 20mM MgCl2 and 1mM DTT at pH 7.5. Used a 24-well plate sealed with Vaseline and total well volumes of 0.402mL. Hanging drops were 0.001mL mother liquor to 0.001mL protein. Mother liquor contained 2.6mM NaCl, 1mM MgCl2, 15.7mM HEPES (pH7.5), 2.5mM DTT, 43.5mM Ca(OAc)2, and 20.5% PEG 3350.

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Data collection

DiffractionMean temperature: 173.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 28216 / % possible obs: 65.5 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.82 Å2 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.018 / Rrim(I) all: 0.028 / Χ2: 1.413 / Net I/σ(I): 38.3 / Num. measured all: 60862
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.561.50.092500.9520.0870.1271.8442.3
1.56-1.581.90.0951900.9540.0870.1291.8228.9
1.58-1.622.10.0783450.9790.0710.1061.5715.8
1.62-1.652.20.0715020.9830.0640.0961.46123.3
1.65-1.682.20.0647000.9840.0580.0871.56232.7
1.68-1.722.20.069950.9880.0540.0821.66245.5
1.72-1.772.20.05413240.9870.0490.0731.70561.9
1.77-1.812.20.04918830.990.0450.0671.69686.5
1.81-1.872.20.04319320.9930.0390.0591.65991
1.87-1.9320.04214580.9930.0390.0572.22367.2
1.93-22.10.03618580.9940.0330.0491.83185.4
2-2.082.20.03119840.9960.0280.0411.56392.9
2.08-2.172.20.02720090.9970.0240.0361.40493.3
2.17-2.2920.02610620.9970.0240.0361.56949.2
2.29-2.432.20.02120090.9980.0190.0291.08893.6
2.43-2.622.20.01920460.9990.0170.0250.98995.1
2.62-2.882.20.01720660.9990.0160.0240.99695.6
2.88-3.32.20.01720860.9980.0150.0230.9896.7
3.3-4.1520.01715990.9980.0150.0231.06574.1
4.15-502.20.01821180.9980.0170.0241.33798.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8Y

3k8y


Resolution: 1.532→36.137 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2005 7.11 %random selection
Rwork0.1583 26208 --
obs0.1614 28213 65.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.42 Å2 / Biso mean: 21.1152 Å2 / Biso min: 10.08 Å2
Refinement stepCycle: final / Resolution: 1.532→36.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 62 336 3005
Biso mean--17.26 26.87 -
Num. residues----332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062745
X-RAY DIFFRACTIONf_angle_d0.9143736
X-RAY DIFFRACTIONf_chiral_restr0.051420
X-RAY DIFFRACTIONf_plane_restr0.004486
X-RAY DIFFRACTIONf_dihedral_angle_d11.9472267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5324-1.57070.3586100.25681345
1.5707-1.61320.3258290.199338914
1.6132-1.66060.2556640.186672326
1.6606-1.71420.2432950.1774111340
1.7142-1.77550.22431410.1889178663
1.7755-1.84660.23391940.1908256590
1.8466-1.93060.21691520.1725202871
1.9306-2.03240.23031800.1719259191
2.0324-2.15970.21352090.1675263993
2.1597-2.32640.19731260.1684174862
2.3264-2.56050.23792050.1697269994
2.5605-2.93090.24072110.1698271296
2.9309-3.6920.1721910.1445253489
3.692-36.1370.15831980.1299254789

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