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- PDB-8zo0: Samll GTPase RhoA Y42C mutant in complex with GTP analogue -

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Basic information

Entry
Database: PDB / ID: 8zo0
TitleSamll GTPase RhoA Y42C mutant in complex with GTP analogue
ComponentsTransforming protein RhoA
KeywordsCELL INVASION / Small GTPase RhoA / Y42C mutant / GTP-bound state
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 modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / myosin binding / regulation of neuron projection development / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / ruffle membrane / neuron migration / G beta:gamma signalling through PI3Kgamma / Ovarian tumor domain proteases / cell junction
Similarity search - Function
Small GTPase Rho / small GTPase Rho family 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 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsJiang, H. / Wu, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Magnesium Ion Locking RhoA Mutant in Highly Dynamic Cycling Conformations
Authors: Wu, H. / Jiang, H.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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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)21,0113
Polymers20,4641
Non-polymers5472
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.278, 63.682, 81.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20464.479 Da / Num. of mol.: 1 / Mutation: Y42C
Source method: isolated from a genetically manipulated source
Details: 20.438 kDa / Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586, 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 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 5.5), 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97867 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2.21→40.8 Å / Num. obs: 8444 / % possible obs: 95.2 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.001 / Net I/σ(I): 24.4
Reflection shellResolution: 2.21→2.29 Å / Rmerge(I) obs: 0.0001 / Num. unique obs: 458

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286)refinement
PHENIX(1.21.1_5286)phasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTN

1ftn


Resolution: 2.21→34.35 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 --
Rwork0.1836 --
obs-8280 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 33 77 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.851
X-RAY DIFFRACTIONf_dihedral_angle_d17.475584
X-RAY DIFFRACTIONf_chiral_restr0.055219
X-RAY DIFFRACTIONf_plane_restr0.008256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.530.26531190.17412260X-RAY DIFFRACTION82
2.53-3.190.26681580.20172697X-RAY DIFFRACTION98
3.19-34.350.22251420.17572904X-RAY DIFFRACTION99

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