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- PDB-10dc: H-Ras GTPase R68A bound to GppNHp -

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Basic information

Entry
Database: PDB / ID: 10dc
TitleH-Ras GTPase R68A bound to GppNHp
ComponentsGTPase HRas
KeywordsHYDROLASE / SIGNALING PROTEIN / small GTPase / Ras GTPase / GTP analog
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 / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / adipose tissue development / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / 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 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / 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 / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 KD Mutants / positive regulation of JNK cascade / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / endocytosis / chemotaxis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / RAS processing / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cellular senescence / GDP binding / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling / MAPK cascade / T cell receptor signaling pathway / regulation of cell population proliferation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade
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 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: 2.08 Å
AuthorsKnihtila, R. / Marcus, K. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1517295 United States
CitationJournal: J.Biol.Chem.
Title: An evolutionarily conserved salt bridge stabilizes the active site for GTP hydrolysis in Rho GTPases
Authors: Marcus, K. / Schwabe, M. / Knihtila, R. / Mattos, C.
History
DepositionJan 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3363
Polymers18,7891
Non-polymers5472
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.896, 69.896, 33.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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


Mass: 18789.076 Da / Num. of mol.: 1 / Mutation: R68A
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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Acetate, 20% w/v PEG 3350, 0.1% N-octyl glucopyranoside

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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: Jan 6, 2016
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.08→23.3 Å / Num. obs: 9861 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.107 / Net I/σ(I): 27.5
Reflection shellResolution: 2.08→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.413 / Num. unique obs: 1385 / CC1/2: 0.969 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→23.3 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 987 10.01 %
Rwork0.1646 8874 -
obs0.1697 9861 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 2.08→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 33 126 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00351298
X-RAY DIFFRACTIONf_angle_d0.55281766
X-RAY DIFFRACTIONf_chiral_restr0.044203
X-RAY DIFFRACTIONf_plane_restr0.0054225
X-RAY DIFFRACTIONf_dihedral_angle_d16.156490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.190.26581380.17811247X-RAY DIFFRACTION99.93
2.19-2.330.23721340.15681259X-RAY DIFFRACTION99.64
2.33-2.510.25611450.1741253X-RAY DIFFRACTION99.86
2.51-2.760.23911360.17651265X-RAY DIFFRACTION99.93
2.76-3.160.22621440.16971248X-RAY DIFFRACTION99.93
3.16-3.970.18661400.151280X-RAY DIFFRACTION99.93
3.98-23.30.19611500.16561322X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.97526147612-0.204149714271-0.08998572608210.8806181595330.2605705525190.5916847173-0.0209546829261-0.20312907483-0.3658904237880.1327076817160.06650593952580.1074152749230.1484688316420.0713065131877-0.0721092050940.2456206125340.00544291489699-0.003207071660790.213327933490.01543579607220.223655675617-20.8033814268.594092965133.61606218318
20.6243901135190.7871410798651.043590584161.331468252620.8067896986183.85996570292-0.0053228610313-0.1621316078660.1777878699450.228477434692-0.07851594938150.4569278661750.074855346899-0.7433394311650.03455019698430.375963638366-0.006223796836160.04081703296180.3862221191260.04159755376820.413504600669-33.05146632776.770269524373.53964204887
30.329676516784-0.402285758433-0.1881332499890.7733789418010.4713688805781.10707880467-0.0865659429182-0.104908488263-0.04522533348490.04906351240260.01360685776340.13870553754-0.11152772185-0.06670015338910.04870140663180.2233606273910.0169346297898-0.009479214333620.2153216185960.0047684562920.194587374351-17.17296256578.068900221088.36484264322
41.44462043516-0.2511976638680.1074339035791.30789489690.3405954622571.45177947043-0.0396854383231-0.01302960749250.1509971436980.04229074228970.0397284821373-0.0934061307986-0.1730855088360.218416973816-0.02944926346950.174104477902-0.01470959001940.01018477303050.198005126013-0.008058511660680.209776285391-22.081560474622.24787838432.12671474646
51.295129577040.7353874378180.09440022746651.609800987740.3478826443561.023320442440.03247989678240.06487150194690.0663904401535-0.06598220219380.08694229569820.0643107875042-0.0866957398413-0.0691752231731-0.1079849885370.2092051682460.0244116241350.008498249201520.2149479175220.003256815242430.210430798096-21.496287973620.3793759484-6.65900691848
63.50191460675-0.22829781792-0.09315897596811.13541221537-0.6107219876371.18554074869-0.1115072442340.10559406202-0.0528063231314-0.09191002346240.0261769179966-0.100761107369-0.06334170684180.0002591833641950.092605316330.2270692052220.00409680575514-0.003510938951990.225214767175-0.00410522779310.172219130325-11.781051320912.0719337027-2.65734179659
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 25 )1 - 251 - 25
22chain 'A' and (resid 26 through 36 )26 - 3626 - 36
33chain 'A' and (resid 37 through 74 )37 - 7437 - 70
44chain 'A' and (resid 75 through 126 )75 - 12671 - 122
55chain 'A' and (resid 127 through 151 )127 - 151123 - 147
66chain 'A' and (resid 152 through 166 )152 - 166148 - 162

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