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- PDB-6v6v: Crystal structure of oncogenic RhoA mutant G14V complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 6v6v
TitleCrystal structure of oncogenic RhoA mutant G14V complexed with GDP
ComponentsTransforming protein RhoA
KeywordsHYDROLASE / GTPase / Switch I / Switch II
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway ...alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / stress fiber assembly / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / positive regulation of protein serine/threonine kinase activity / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / mitotic spindle assembly / ficolin-1-rich granule membrane / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / Rho protein signal transduction / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / substrate adhesion-dependent cell spreading / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / positive regulation of neuron differentiation / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / secretory granule membrane / cell periphery / regulation of actin cytoskeleton organization / regulation of microtubule cytoskeleton organization / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / ruffle membrane / cytoplasmic side of plasma membrane / Ovarian tumor domain proteases / G beta:gamma signalling through PI3Kgamma / cell migration / lamellipodium / cellular response to lipopolysaccharide / G alpha (12/13) signalling events / actin cytoskeleton organization / G protein activity / midbody / cell cortex / vesicle / dendritic spine / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / postsynapse / endosome / focal adhesion / GTPase activity / Neutrophil degranulation
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
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: 1.4 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

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2645
Polymers20,6211
Non-polymers6444
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.225, 86.924, 34.078
Angle α, β, γ (deg.)90.000, 95.200, 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: 20620.596 Da / Num. of mol.: 1 / Fragment: C-terminal trancated at residue 181 / Mutation: G14V, 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


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


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.31 Å3/Da / Density % sol: 46.64 % / Mosaicity: 0.02 °
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: Mar 16, 2017
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: 1.4→25.817 Å / Num. all: 36248 / Num. obs: 36248 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.168 / Rrim(I) all: 0.326 / Rsym value: 0.237 / Net I/av σ(I): 1.4 / Net I/σ(I): 2.8 / Num. measured all: 131266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.482.70.8280.91301549040.6541.0920.8280.992.7
1.48-1.573.60.5791.21837650370.4240.8140.5791.5100
1.57-1.673.80.421.61795147790.30.5840.422100
1.67-1.813.80.33221680544520.2340.4540.3322.6100
1.81-1.983.80.2752.11543440570.1980.3860.2753.3100
1.98-2.213.80.2532.21418237120.1770.3460.2533.8100
2.21-2.563.80.2482.41246932470.170.3330.2484.2100
2.56-3.133.80.2312.51064227710.160.3150.2314.4100
3.13-4.433.80.2142.6826121460.1470.2880.2144.6100
4.43-25.8173.60.1952.9413111430.1420.2720.1954.495.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1FTN

1ftn


Resolution: 1.4→24.45 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 2008 5.54 %
Rwork0.2018 34211 -
obs0.203 36219 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.54 Å2 / Biso mean: 29.248 Å2 / Biso min: 8.89 Å2
Refinement stepCycle: final / Resolution: 1.4→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 41 178 1637
Biso mean--24.87 36.21 -
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 (%)
1.4-1.440.38061310.36592136226789
1.44-1.470.33231460.3252381252796
1.47-1.520.28051350.290424512586100
1.52-1.570.27791520.257724602612100
1.57-1.620.29851410.226725112652100
1.62-1.690.23591470.22824652612100
1.69-1.760.23321530.205924382591100
1.76-1.860.23241390.199424912630100
1.86-1.970.22231450.200624692614100
1.97-2.130.21641520.195225012653100
2.13-2.340.19381430.188324512594100
2.34-2.680.2241370.195524952632100
2.68-3.370.20781460.186424782624100
3.37-24.450.19691410.17332484262598
Refinement TLS params.Method: refined / Origin x: 3.5724 Å / Origin y: 2.9723 Å / Origin z: 1.9617 Å
111213212223313233
T0.0855 Å2-0.0054 Å2-0.0004 Å2-0.0971 Å2-0.004 Å2--0.0767 Å2
L0.7377 °20.1673 °2-0.0578 °2-3.5262 °2-1.2314 °2--1.7124 °2
S-0.0023 Å °0.0075 Å °0.0184 Å °0.0363 Å °-0.0832 Å °-0.0913 Å °-0.024 Å °-0.0012 Å °0.0362 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 - 178

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