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- PDB-6v6u: Crystal structure of RhoA-GDP with novel Switch I conformation -

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Basic information

Entry
Database: PDB / ID: 6v6u
TitleCrystal structure of RhoA-GDP with novel Switch I conformation
ComponentsTransforming protein RhoA
KeywordsHYDROLASE / GTPase / Switch I / Switch II
Function / homology
Function and homology information


aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 ...aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 / regulation of systemic arterial blood pressure by endothelin / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / 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 / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / secretory granule membrane / 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 / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway / 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
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 Å
AuthorsLin, Y. / Zheng, Y.
CitationJournal: Structure / Year: 2021
Title: Structure of an inactive conformation of GTP-bound RhoA GTPase.
Authors: Lin, Y. / Lu, S. / Zhang, J. / Zheng, Y.
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,2225
Polymers20,5791
Non-polymers6444
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.216, 87.192, 34.271
Angle α, β, γ (deg.)90.000, 95.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20578.518 Da / Num. of mol.: 1 / Fragment: C-terminal trancated at residue 181 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX-2T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61586, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 20-24% PEG8K, 15% Dioxane, 0.1M Tris pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationMonochromator: Kohzu HLD-4 Double Crystal water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.16→87.19 Å / Num. obs: 64753 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Net I/σ(I): 9.1
Reflection shellResolution: 1.16→1.22 Å / Rmerge(I) obs: 0.446 / Num. unique obs: 9359 / Rpim(I) all: 0.323 / Rrim(I) all: 0.624

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1FTN

1ftn


Resolution: 1.16→34.14 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 1999 3.09 %
Rwork0.1701 62700 -
obs0.1705 64699 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.23 Å2 / Biso mean: 20.6756 Å2 / Biso min: 6.37 Å2
Refinement stepCycle: final / Resolution: 1.16→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 41 201 1657
Biso mean--18.16 30.47 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.16-1.190.28361210.24484434455597
1.19-1.220.22211640.22524413457798
1.22-1.250.2461370.21364446458398
1.25-1.290.21891340.19624466460098
1.29-1.340.20881510.18844441459298
1.34-1.390.19461460.18264470461699
1.39-1.460.1921380.16944524466299
1.46-1.530.17521450.15894520466599
1.53-1.630.15761430.14914507465099
1.63-1.760.18331500.154344994649100
1.76-1.930.18841430.162845144657100
1.93-2.210.17131410.162745394680100
2.21-2.790.18831390.16984512465199
2.79-34.140.16711470.16154415456296
Refinement TLS params.Method: refined / Origin x: 3.5509 Å / Origin y: 2.7295 Å / Origin z: 1.9344 Å
111213212223313233
T0.0534 Å2-0.0038 Å20.0132 Å2-0.0629 Å2-0.0056 Å2--0.0517 Å2
L0.7414 °2-0.0274 °20.1153 °2-2.4802 °2-0.6007 °2--1.1318 °2
S0.0063 Å °-0.0042 Å °0.0325 Å °0.0444 Å °-0.0331 Å °0.0235 Å °-0.0405 Å °-0.0177 Å °0.0241 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 181
2X-RAY DIFFRACTION1allA200
3X-RAY DIFFRACTION1allA300
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allS1 - 201

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