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- PDB-9n4c: RhoA GTPase E102A bound to GTPgammaS -

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Basic information

Entry
Database: PDB / ID: 9n4c
TitleRhoA GTPase E102A 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 / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / forebrain radial glial cell differentiation / regulation of modification of postsynaptic structure / cell junction assembly / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / regulation of systemic arterial blood pressure by endothelin / negative regulation of motor neuron apoptotic process / negative regulation of oxidative phosphorylation / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / negative regulation of cell size / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / androgen receptor signaling pathway / stress fiber assembly / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / positive regulation of protein serine/threonine kinase activity / ficolin-1-rich granule membrane / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / skeletal muscle tissue development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Rho protein signal transduction / GPVI-mediated activation cascade / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / substantia nigra development / regulation of cell migration / regulation of microtubule cytoskeleton organization / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / cell periphery / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / VEGFA-VEGFR2 Pathway / cytoplasmic side of plasma membrane / ruffle membrane / neuron migration / cell morphogenesis / Ovarian tumor domain proteases / cell junction / G beta:gamma signalling through PI3Kgamma
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 / IODIDE ION / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Transforming protein RhoA
C: Transforming protein RhoA
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,31460
Polymers81,6384
Non-polymers6,67656
Water10,755597
1
A: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,78513
Polymers20,4091
Non-polymers1,37512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,33021
Polymers20,4091
Non-polymers1,92120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,66710
Polymers20,4091
Non-polymers1,2589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,53116
Polymers20,4091
Non-polymers2,12215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.217, 60.532, 67.134
Angle α, β, γ (deg.)67.842, 78.049, 68.362
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 20409.422 Da / Num. of mol.: 4 / Mutation: E102A
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

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Non-polymers , 6 types, 653 molecules

#2: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2 uL protein (8 mg/mL RhoA E102A bound to GTPgammaS, 25 mM Tris-HCl pH 8.0, 2 mM MgCl2, 10 mM BME) + 2 uL of crystallization solution over 500 uL reservoir of crystallization solution. ...Details: 2 uL protein (8 mg/mL RhoA E102A bound to GTPgammaS, 25 mM Tris-HCl pH 8.0, 2 mM MgCl2, 10 mM BME) + 2 uL of crystallization solution over 500 uL reservoir of crystallization solution. Crystallization solution: 0.2 M Ammonium iodide, 20% PEG 3,350

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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: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→44.26 Å / Num. obs: 53737 / % possible obs: 96.26 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.07 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.09267 / Rpim(I) all: 0.019 / Rrim(I) all: 0.1311 / Net I/σ(I): 27.53
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 8.85 / Num. unique obs: 3053 / CC1/2: 0.949 / CC star: 0.934 / Rpim(I) all: 0.093 / Rrim(I) all: 0.348 / % possible all: 68.39

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.26 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.7461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 3409 6.34 %
Rwork0.1766 50328 -
obs0.1794 53737 82.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 180 597 6414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725894
X-RAY DIFFRACTIONf_angle_d0.97438021
X-RAY DIFFRACTIONf_chiral_restr0.0559886
X-RAY DIFFRACTIONf_plane_restr0.00871032
X-RAY DIFFRACTIONf_dihedral_angle_d14.3192238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32811180.26251730X-RAY DIFFRACTION68.44
2.33-2.360.34151270.24321874X-RAY DIFFRACTION73.24
2.36-2.40.27741270.24661938X-RAY DIFFRACTION74.01
2.4-2.440.29151250.22871881X-RAY DIFFRACTION75.24
2.44-2.480.26331410.23642007X-RAY DIFFRACTION76.55
2.48-2.530.29621230.22461918X-RAY DIFFRACTION77.49
2.53-2.580.29071480.22942050X-RAY DIFFRACTION78.67
2.58-2.630.26011360.22082004X-RAY DIFFRACTION79.49
2.63-2.690.28641380.2182035X-RAY DIFFRACTION80.72
2.69-2.750.30451330.22832063X-RAY DIFFRACTION80.56
2.75-2.820.26681410.21692114X-RAY DIFFRACTION82.3
2.82-2.890.29491440.21342067X-RAY DIFFRACTION81.65
2.89-2.980.22961430.20792110X-RAY DIFFRACTION83.26
2.98-3.080.24571370.19872160X-RAY DIFFRACTION83.59
3.08-3.180.25941510.19382156X-RAY DIFFRACTION84.26
3.19-3.310.20891410.17092150X-RAY DIFFRACTION85.04
3.31-3.460.22371450.15542156X-RAY DIFFRACTION85.79
3.46-3.650.20721500.15642244X-RAY DIFFRACTION86.24
3.65-3.870.18721550.14772190X-RAY DIFFRACTION86.98
3.87-4.170.17211490.13252246X-RAY DIFFRACTION87.79
4.17-4.590.15041540.12872267X-RAY DIFFRACTION88.68
4.59-5.250.17241620.13512283X-RAY DIFFRACTION90.22
5.26-6.620.19181590.16722323X-RAY DIFFRACTION91.05
6.62-44.260.19131620.17212362X-RAY DIFFRACTION92.39

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