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- PDB-7jih: HRAS A59E GppNHp -

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Basic information

Entry
Database: PDB / ID: 7jih
TitleHRAS A59E GppNHp
ComponentsGTPase HRas
KeywordsONCOPROTEIN / Mutant Cancer GTPase
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 / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / myelination / GRB2 events in EGFR 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 / Ras activation upon Ca2+ influx through NMDA receptor / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / animal organ morphogenesis / 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: 1.989 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
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Characterization of KRAS4B A59E and A59T oncogenic alleles suggest a novel small GTPase function
Authors: Johnson, C.W. / 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)39,1448
Polymers37,8662
Non-polymers1,2776
Water1,838102
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5724
Polymers18,9331
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5724
Polymers18,9331
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.675, 49.832, 57.320
Angle α, β, γ (deg.)90.000, 117.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTPase 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Starting concentration of HRAS A59T GppNHp was 18.1mg/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 18.1mg/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, 9.95mM Ca(OAc)2, and 19.9% 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: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.989→50 Å / Num. obs: 15450 / % possible obs: 80.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.18 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.051 / Rrim(I) all: 0.098 / Χ2: 0.949 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.989-2.021.40.598630.5970.5260.8010.216.7
2.02-2.061.40.5881210.7520.4710.7590.26112.6
2.06-2.11.40.3982470.8440.3120.510.32326.1
2.1-2.141.50.4743920.680.3610.6020.42641.1
2.14-2.191.80.3795680.8560.280.4760.45958.8
2.19-2.242.10.3297260.9020.2350.4080.45876.1
2.24-2.32.50.328690.8720.2160.3890.50490.5
2.3-2.362.90.2869240.9190.1840.3430.47196.4
2.36-2.433.30.2589430.9310.1610.3060.49198.8
2.43-2.513.60.2469460.9410.1450.2870.5699.6
2.51-2.63.60.1999640.9630.1160.2320.54799.8
2.6-2.73.70.1659490.9650.0960.1920.55999.9
2.7-2.823.70.1529730.980.0880.1770.60299.9
2.82-2.973.80.1159540.9870.0670.1330.62599.6
2.97-3.163.80.0949530.9910.0550.1090.81899.2
3.16-3.43.70.089720.9920.0470.0931.04699.6
3.4-3.743.70.0669530.9950.0390.0771.1699.5
3.74-4.293.60.0569640.9950.0340.0661.43798.8
4.29-5.43.50.0589710.9930.0370.0691.96898.5
5.4-503.50.069980.9950.0390.0732.45398.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.11.1-2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8Y

3k8y


Resolution: 1.989→29.17 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1575 10.21 %random selection
Rwork0.196 13845 --
obs0.202 15420 80.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 35.3086 Å2 / Biso min: 17.62 Å2
Refinement stepCycle: final / Resolution: 1.989→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 78 102 2605
Biso mean--33.85 34.55 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072533
X-RAY DIFFRACTIONf_angle_d13435
X-RAY DIFFRACTIONf_chiral_restr0.049394
X-RAY DIFFRACTIONf_plane_restr0.005436
X-RAY DIFFRACTIONf_dihedral_angle_d10.9791509
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.989-2.05290.3854190.33441349
2.0529-2.12630.3497430.281346429
2.1263-2.21140.33411030.264991759
2.2114-2.3120.30991590.2395137488
2.312-2.43380.30421780.2283151698
2.4338-2.58620.2931730.22751569100
2.5862-2.78580.26711720.22041586100
2.7858-3.06580.28631830.21061555100
3.0658-3.50880.24581840.1845156399
3.5088-4.41830.21131720.1627158399
4.4183-29.170.22871890.1793158498

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