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- PDB-8fpx: Crystal structure of tumor related RhoA mutant A161P in complex w... -

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Basic information

Entry
Database: PDB / ID: 8fpx
TitleCrystal structure of tumor related RhoA mutant A161P in complex with GDP
ComponentsTransforming protein RhoA
KeywordsSIGNALING PROTEIN / Hydrolase / Small G proteins / GTPase / fast-cycling mutant / A161P
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 / regulation of osteoblast proliferation ...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 / regulation of osteoblast proliferation / 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 / 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 / beta selection / establishment of epithelial cell apical/basal polarity / 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 / RHO GTPases activate KTN1 / odontogenesis / PCP/CE pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / 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 / positive regulation of cytokinesis / regulation of neuron projection development / RHOC GTPase cycle / cellular response to cytokine stimulus / androgen receptor signaling pathway / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / mitotic spindle assembly / endothelial cell migration / RHOA GTPase cycle / 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 / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / secretory granule membrane / small monomeric GTPase / kidney development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / 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
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLin, Y. / Zheng, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL147536 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL158688 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)U54 DK126108 United States
CitationJournal: Nat Commun / Year: 2024
Title: Tumor-derived RHOA mutants interact with effectors in the GDP-bound state.
Authors: Lin, Y. / Ramelot, T.A. / Senyuz, S. / Gursoy, A. / Jang, H. / Nussinov, R. / Keskin, O. / Zheng, Y.
History
DepositionJan 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)21,1604
Polymers20,6051
Non-polymers5563
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.212, 87.265, 34.044
Angle α, β, γ (deg.)90.00, 95.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20604.555 Da / Num. of mol.: 1 / Mutation: F25N, A161P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX4T / Production host: Bacteria (eubacteria) / Strain (production host): Escherichia coli / Variant (production host): BL21(DE3) / 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: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.31 Å3/Da / Density % sol: 46.82 % / Description: plate
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.47→31.57 Å / Num. obs: 31430 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.93 / Rpim(I) all: 0.148 / Rrim(I) all: 0.286 / Net I/av σ(I): 3 / Net I/σ(I): 3
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4322 / CC1/2: 0.446 / Rpim(I) all: 0.64 / Rrim(I) all: 1.075 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTN

1ftn


Resolution: 1.47→31.57 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 1993 6.35 %
Rwork0.1914 --
obs0.1935 31397 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 35 197 1649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061540
X-RAY DIFFRACTIONf_angle_d0.932101
X-RAY DIFFRACTIONf_dihedral_angle_d16.381608
X-RAY DIFFRACTIONf_chiral_restr0.088228
X-RAY DIFFRACTIONf_plane_restr0.007276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.37351250.33171870X-RAY DIFFRACTION89
1.51-1.550.33871380.30672086X-RAY DIFFRACTION97
1.55-1.590.33361430.26152099X-RAY DIFFRACTION100
1.59-1.640.23721420.23982119X-RAY DIFFRACTION100
1.64-1.70.25751450.22052153X-RAY DIFFRACTION100
1.7-1.770.23471440.19582086X-RAY DIFFRACTION100
1.77-1.850.19811470.21012112X-RAY DIFFRACTION100
1.85-1.950.23281310.18012130X-RAY DIFFRACTION100
1.95-2.070.20761500.17262112X-RAY DIFFRACTION100
2.07-2.230.2021480.17582128X-RAY DIFFRACTION100
2.23-2.460.2361450.18012147X-RAY DIFFRACTION100
2.46-2.810.2411520.1922104X-RAY DIFFRACTION100
2.81-3.540.1911450.17142131X-RAY DIFFRACTION100
3.54-31.570.19821380.16892127X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 3.7551 Å / Origin y: 3.0414 Å / Origin z: 2.115 Å
111213212223313233
T0.0824 Å2-0.0073 Å20.053 Å2-0.1088 Å2-0.0023 Å2--0.0875 Å2
L0.5708 °20.1704 °20.0352 °2-2.2842 °2-0.7519 °2--1.1972 °2
S-0.006 Å °0.0031 Å °0.0182 Å °0.0549 Å °-0.0603 Å °-0.0133 Å °-0.0401 Å °-0.0159 Å °0.0475 Å °
Refinement TLS groupSelection details: all

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