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- PDB-6kx3: Crystal structure of RhoA protein with covalent inhibitor DC-Rhoin -

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Basic information

Entry
Database: PDB / ID: 6kx3
TitleCrystal structure of RhoA protein with covalent inhibitor DC-Rhoin
ComponentsTransforming protein RhoA
KeywordsCELL INVASION / inhibitor / covalent / complex
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
Chem-8ZO / GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsZhang, H. / Luo, C.
CitationJournal: Adv Sci / Year: 2020
Title: Covalent Inhibitors Allosterically Block the Activation of Rho Family Proteins and Suppress Cancer Cell Invasion.
Authors: Sun, Z. / Zhang, H. / Zhang, Y. / Liao, L. / Zhou, W. / Zhang, F. / Lian, F. / Huang, J. / Xu, P. / Zhang, R. / Lu, W. / Zhu, M. / Tao, H. / Yang, F. / Ding, H. / Chen, S. / Yue, L. / Zhou, ...Authors: Sun, Z. / Zhang, H. / Zhang, Y. / Liao, L. / Zhou, W. / Zhang, F. / Lian, F. / Huang, J. / Xu, P. / Zhang, R. / Lu, W. / Zhu, M. / Tao, H. / Yang, F. / Ding, H. / Chen, S. / Yue, L. / Zhou, B. / Zhang, N. / Tan, M. / Jiang, H. / Chen, K. / Liu, B. / Liu, C. / Dang, Y. / Luo, C.
History
DepositionSep 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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)21,1373
Polymers20,4411
Non-polymers6952
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-5 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.784, 91.784, 55.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 20441.330 Da / Num. of mol.: 1 / Mutation: C16V, C20S, C83V, C159T
Source method: isolated from a genetically manipulated source
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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-8ZO / prop-2-enyl (3R)-1,1-bis(oxidanylidene)-2,3-dihydro-1-benzothiophene-3-carboxylate


Mass: 252.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10 mg/mL mutant, 0.2M NaCl, 0.1M acetate Na (pH 4.5), 1.26M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.981→45.892 Å / Num. obs: 17117 / % possible obs: 100 % / Redundancy: 28.6 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.07104 / Net I/σ(I): 46.17
Reflection shellResolution: 1.981→2.052 Å / Rmerge(I) obs: 0.6719 / Num. unique obs: 1670 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTN

1ftn


Resolution: 1.981→45.892 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.92
RfactorNum. reflection% reflection
Rfree0.2677 838 4.9 %
Rwork0.2207 --
obs0.223 17114 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.85 Å2 / Biso mean: 41.2361 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 1.981→45.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 45 82 1477
Biso mean--40.23 45.35 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081424
X-RAY DIFFRACTIONf_angle_d1.0361932
X-RAY DIFFRACTIONf_chiral_restr0.068214
X-RAY DIFFRACTIONf_plane_restr0.006245
X-RAY DIFFRACTIONf_dihedral_angle_d18.359851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9811-2.10530.29461390.25662652
2.1053-2.26780.31071300.25012660
2.2678-2.4960.31321410.24872677
2.496-2.85710.30141440.24672681
2.8571-3.59950.26841410.22952731
3.5995-45.8920.23551430.19282875

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