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- PDB-8gi6: Crystal structure of RhoA mutant L69R complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 8gi6
TitleCrystal structure of RhoA mutant L69R complexed with GDP
ComponentsTransforming protein RhoA
KeywordsHYDROLASE / Small GTPase
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 / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / establishment of epithelial cell apical/basal polarity / beta selection / negative regulation of cell size / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / positive regulation of podosome assembly / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / odontogenesis / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / endothelial cell migration / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / skeletal muscle tissue development / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / secretory granule membrane / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / cell morphogenesis / positive regulation of protein serine/threonine kinase activity / G protein activity / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / positive regulation of non-canonical NF-kappaB signal transduction / G beta:gamma signalling through PI3Kgamma / G alpha (12/13) signalling events
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
GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, X. / Qian, X. / Chandravanshi, M. / Lowy, D.R. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
CitationJournal: To be published
Title: Ras-like GTPases mutant structures
Authors: Chen, X. / Qian, X. / Chandravanshi, M. / Lowy, D.R. / Walters, K.J.
History
DepositionMar 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Structure summary / Category: struct / Item: _struct.title

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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)22,5783
Polymers22,1111
Non-polymers4682
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.960, 64.187, 83.078
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: 22110.518 Da / Num. of mol.: 1 / Mutation: L69R
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) / References: UniProt: P61586, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*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.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 5.7
Details: 0.1 M Na acetate (pH 5.7), 0.5 mM Na citrate, 26% PEG4000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 18, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→41.54 Å / Num. obs: 34454 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.99 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Net I/σ(I): 10.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 3370 / CC1/2: 0.96 / Rpim(I) all: 0.11 / Rrim(I) all: 0.285 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPv11.0phasing
REFMACv5.0refinement
Cootv0.9.8.3model building
PDB_EXTRACTv4.0data extraction
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.787 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18173 1756 5.1 %RANDOM
Rwork0.15306 ---
obs0.15448 32623 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.222 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--0.66 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.4→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 29 182 1627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131495
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151415
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.6842033
X-RAY DIFFRACTIONr_angle_other_deg1.4991.5983280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17822.59381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34515266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3441.042721
X-RAY DIFFRACTIONr_mcbond_other1.3241.037720
X-RAY DIFFRACTIONr_mcangle_it1.9871.561901
X-RAY DIFFRACTIONr_mcangle_other1.9991.566902
X-RAY DIFFRACTIONr_scbond_it2.5381.343774
X-RAY DIFFRACTIONr_scbond_other2.5511.35766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9531.9071117
X-RAY DIFFRACTIONr_long_range_B_refined4.68512.9861681
X-RAY DIFFRACTIONr_long_range_B_other4.5812.5031635
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 122 -
Rwork0.16 2380 -
obs--99.64 %

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