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- PDB-9n4b: RhoA GTPase R70A bound to GTPgammaS -

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Basic information

Entry
Database: PDB / ID: 9n4b
TitleRhoA GTPase R70A bound to GTPgammaS
ComponentsTransforming protein RhoA
KeywordsHYDROLASE / small GTPase / Rho GTPase / GTP analog
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway ...alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / ficolin-1-rich granule membrane / Rho protein signal transduction / RHOA GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / GPVI-mediated activation cascade / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / secretory granule membrane / regulation of actin cytoskeleton organization / cell periphery / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium / cellular response to lipopolysaccharide / G alpha (12/13) signalling events / midbody / G protein activity / cell cortex / vesicle / dendritic spine / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / postsynapse / endosome / focal adhesion / GTPase activity / Neutrophil degranulation
Similarity search - Function
Small GTPase Rho / Small GTPase Rho 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMarcus, K. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1517295 United States
CitationJournal: J.Biol.Chem. / Year: 2026
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
DepositionFeb 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2026Group: 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: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2587
Polymers20,3101
Non-polymers9486
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.988, 59.988, 150.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20310.264 Da / Num. of mol.: 1 / Mutation: R70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61586, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2 uL protein (8 mg/mL RhoA R70A bound to GTPgammaS in 25 mM Tris-HCl pH8.0, 2 mM MgCl2, and 10 mM BME) + 2 uL crystallization reagent sitting above 500 uL crystallization reagent. ...Details: 2 uL protein (8 mg/mL RhoA R70A bound to GTPgammaS in 25 mM Tris-HCl pH8.0, 2 mM MgCl2, and 10 mM BME) + 2 uL crystallization reagent sitting above 500 uL crystallization reagent. Crystallization reagent: 250 mM ammonium sulfate, 1.50 M lithium sulfate, and 100 mM sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 16, 2016
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→32.41 Å / Num. obs: 13211 / % possible obs: 94.37 % / Redundancy: 1.8 % / Biso Wilson estimate: 59.11 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.05431 / Rrim(I) all: 0.0768 / Net I/σ(I): 10.82
Reflection shellResolution: 3→3.107 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2365 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 1150 / CC1/2: 0.95 / CC star: 0.987 / % possible all: 86.61

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→32.41 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 565 9.99 %
Rwork0.1991 --
obs0.2042 5653 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 53 8 1451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091468
X-RAY DIFFRACTIONf_angle_d1.1612003
X-RAY DIFFRACTIONf_dihedral_angle_d8.041205
X-RAY DIFFRACTIONf_chiral_restr0.061220
X-RAY DIFFRACTIONf_plane_restr0.007255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.36281250.26831120X-RAY DIFFRACTION87
3.3-3.780.33891370.24041236X-RAY DIFFRACTION94
3.78-4.760.20091460.181320X-RAY DIFFRACTION99
4.76-32.410.20721570.17251412X-RAY DIFFRACTION98

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