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- PDB-7dph: H-Ras Q61H in complex with GppNHp (state 1) after structural tran... -

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Basic information

Entry
Database: PDB / ID: 7dph
TitleH-Ras Q61H in complex with GppNHp (state 1) after structural transition by humidity control
ComponentsGTPase HRas
KeywordsONCOPROTEIN / State transition / Ras
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / negative regulation of GTPase activity / 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 ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / negative regulation of GTPase activity / 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 / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / adipose tissue development / positive regulation of MAP kinase activity / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / Schwann cell development / 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 / protein-membrane adaptor activity / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / positive regulation of GTPase activity / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / 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 / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of epithelial cell proliferation / VEGFR2 mediated cell proliferation / animal organ morphogenesis / small monomeric GTPase / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / cellular response to gamma radiation / MAP2K and MAPK activation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / Regulation of RAS by GAPs / RAS processing / chemotaxis / 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 / MAPK cascade / insulin receptor signaling pathway / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsTaniguchi, H. / Matsumoto, S. / Kawamura, T. / Kumasaka, T. / Kataoka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17K15106 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Oncogenic mutations Q61L and Q61H confer active form-like structural features to the inactive state (state 1) conformation of H-Ras protein.
Authors: Matsumoto, S. / Taniguchi-Tamura, H. / Araki, M. / Kawamura, T. / Miyamoto, R. / Tsuda, C. / Shima, F. / Kumasaka, T. / Okuno, Y. / Kataoka, T.
History
DepositionDec 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,8905
Polymers19,2971
Non-polymers5944
Water1,856103
1
A: GTPase HRas
hetero molecules

A: GTPase HRas
hetero molecules

A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,67115
Polymers57,8903
Non-polymers1,78112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area2090 Å2
ΔGint-20 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.769, 91.769, 121.268
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-202-

MG

21A-333-

HOH

31A-401-

HOH

41A-403-

HOH

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Components

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


Mass: 19296.664 Da / Num. of mol.: 1 / Mutation: Q61H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG400, SODIUM ACETATE, CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 29269 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 68.4
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 9.3 / Num. unique obs: 1676

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k8y

3k8y


Resolution: 1.54→23.208 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.168 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2023 1406 4.815 %
Rwork0.1922 27793 -
all0.193 --
obs-29199 99.761 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.994 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.54→23.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 35 103 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131417
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171289
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.6921946
X-RAY DIFFRACTIONr_angle_other_deg1.251.5953008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45622.65183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4731511
X-RAY DIFFRACTIONr_chiral_restr0.0540.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
X-RAY DIFFRACTIONr_nbd_refined0.2010.2253
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.21173
X-RAY DIFFRACTIONr_nbtor_refined0.1470.2644
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.295
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.214
X-RAY DIFFRACTIONr_nbd_other0.1390.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.222
X-RAY DIFFRACTIONr_mcbond_it0.851.852676
X-RAY DIFFRACTIONr_mcbond_other0.8411.849675
X-RAY DIFFRACTIONr_mcangle_it1.4932.763855
X-RAY DIFFRACTIONr_mcangle_other1.4932.765856
X-RAY DIFFRACTIONr_scbond_it0.9851.978741
X-RAY DIFFRACTIONr_scbond_other0.9841.978739
X-RAY DIFFRACTIONr_scangle_it1.6022.9231078
X-RAY DIFFRACTIONr_scangle_other1.6042.9231076
X-RAY DIFFRACTIONr_lrange_it3.52221.3311574
X-RAY DIFFRACTIONr_lrange_other3.40521.0991553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.245990.2222023X-RAY DIFFRACTION100
1.58-1.6230.262830.212006X-RAY DIFFRACTION100
1.623-1.670.224870.2081960X-RAY DIFFRACTION100
1.67-1.7210.213880.2041854X-RAY DIFFRACTION100
1.721-1.7770.195910.2021808X-RAY DIFFRACTION100
1.777-1.8390.191820.1931777X-RAY DIFFRACTION100
1.839-1.9080.207720.1951725X-RAY DIFFRACTION100
1.908-1.9850.199760.1881622X-RAY DIFFRACTION100
1.985-2.0730.202920.1831570X-RAY DIFFRACTION99.9399
2.073-2.1740.196870.1781490X-RAY DIFFRACTION100
2.174-2.290.186720.1831445X-RAY DIFFRACTION100
2.29-2.4280.183700.1881350X-RAY DIFFRACTION100
2.428-2.5930.214860.1891252X-RAY DIFFRACTION100
2.593-2.7980.194770.1971191X-RAY DIFFRACTION100
2.798-3.0610.216570.1971109X-RAY DIFFRACTION99.9143
3.061-3.4160.175520.187999X-RAY DIFFRACTION100
3.416-3.9310.218310.181921X-RAY DIFFRACTION100
3.931-4.7830.202420.167764X-RAY DIFFRACTION99.6292
4.783-6.6350.178400.205600X-RAY DIFFRACTION99.6885
6.635-23.20.252220.27327X-RAY DIFFRACTION87.0324

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