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- PDB-4xh9: CRYSTAL STRUCTURE OF HUMAN RHOA IN COMPLEX WITH DH/PH FRAGMENT OF... -

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Basic information

Entry
Database: PDB / ID: 4xh9
TitleCRYSTAL STRUCTURE OF HUMAN RHOA IN COMPLEX WITH DH/PH FRAGMENT OF THE GUANINE NUCLEOTIDE EXCHANGE FACTOR NET1
Components
  • Neuroepithelial cell-transforming gene 1 protein
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / RHOA GTPASE / ACTIVATOR / GUANINE NUCLEOTIDE EXCHANGE FACTOR
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 / regulation of small GTPase mediated signal transduction / 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 / RHOB GTPase cycle / NRAGE signals death through JNK / 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 Rho protein signal transduction / 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 / positive regulation of GTPase activity / 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 / guanyl-nucleotide exchange factor activity / secretory granule membrane / cellular response to ionizing radiation / 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) / regulation of cell growth / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / cellular response to hydrogen peroxide / 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
Similarity search - Function
Net1, PH domain / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / SOS1/NGEF-like PH domain / Small GTPase Rho / Small GTPase Rho domain profile. ...Net1, PH domain / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / SOS1/NGEF-like PH domain / Small GTPase Rho / Small GTPase Rho domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transforming protein RhoA / Neuroepithelial cell-transforming gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia, C. / Petit, P. / Boutin, J.A. / Ferry, G. / Vuillard, L.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot.
Authors: Petit, A.P. / Garcia-Petit, C. / Bueren-Calabuig, J.A. / Vuillard, L.M. / Ferry, G. / Boutin, J.A.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 10, 2024Group: 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: Neuroepithelial cell-transforming gene 1 protein
B: Transforming protein RhoA
D: Neuroepithelial cell-transforming gene 1 protein
E: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)125,0434
Polymers125,0434
Non-polymers00
Water16,592921
1
A: Neuroepithelial cell-transforming gene 1 protein
B: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,5222
Polymers62,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-16 kcal/mol
Surface area23930 Å2
MethodPISA
2
D: Neuroepithelial cell-transforming gene 1 protein
E: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,5222
Polymers62,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-16 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.100, 101.400, 116.200
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neuroepithelial cell-transforming gene 1 protein / Proto-oncogene p65 Net1 / Rho guanine nucleotide exchange factor 8


Mass: 42232.383 Da / Num. of mol.: 2 / Fragment: UNP residues 149-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NET1, ARHGEF8 / Plasmid: pET28 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: Q7Z628
#2: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20289.164 Da / Num. of mol.: 2 / Fragment: UNP residues 2-180 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pET28 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: P61586
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.86 % / Description: PLATE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bisTris propane pH7.5, 20% PEG3350, 0.2M Tripotassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 83900 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XCG

1xcg


Resolution: 2→34.688 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 4194 5 %
Rwork0.1885 --
obs0.19 83896 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→34.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8269 0 0 921 9190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058473
X-RAY DIFFRACTIONf_angle_d0.90211455
X-RAY DIFFRACTIONf_dihedral_angle_d13.9943265
X-RAY DIFFRACTIONf_chiral_restr0.0331268
X-RAY DIFFRACTIONf_plane_restr0.0061488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.31141370.24092621X-RAY DIFFRACTION100
2.0227-2.04650.27091400.23432652X-RAY DIFFRACTION100
2.0465-2.07150.29721400.232666X-RAY DIFFRACTION100
2.0715-2.09770.23341410.222668X-RAY DIFFRACTION100
2.0977-2.12530.27821400.21142670X-RAY DIFFRACTION100
2.1253-2.15440.25261410.20412676X-RAY DIFFRACTION100
2.1544-2.18520.2421390.20222630X-RAY DIFFRACTION100
2.1852-2.21780.23381380.20582638X-RAY DIFFRACTION100
2.2178-2.25240.24751430.20192709X-RAY DIFFRACTION100
2.2524-2.28940.24031380.20232611X-RAY DIFFRACTION100
2.2894-2.32880.23441400.22677X-RAY DIFFRACTION100
2.3288-2.37120.26521400.19962662X-RAY DIFFRACTION100
2.3712-2.41680.21921400.19742656X-RAY DIFFRACTION100
2.4168-2.46610.25281410.19812679X-RAY DIFFRACTION100
2.4661-2.51970.23231390.1922629X-RAY DIFFRACTION100
2.5197-2.57830.20911410.19262678X-RAY DIFFRACTION100
2.5783-2.64270.23871390.19782642X-RAY DIFFRACTION100
2.6427-2.71420.19561410.22688X-RAY DIFFRACTION100
2.7142-2.7940.22791390.20632641X-RAY DIFFRACTION100
2.794-2.88410.23961410.19932676X-RAY DIFFRACTION100
2.8841-2.98720.23911400.20172668X-RAY DIFFRACTION100
2.9872-3.10670.20581400.1872645X-RAY DIFFRACTION100
3.1067-3.2480.22071400.19052659X-RAY DIFFRACTION100
3.248-3.41910.21211400.18882670X-RAY DIFFRACTION99
3.4191-3.63310.21221400.17812652X-RAY DIFFRACTION99
3.6331-3.91330.1891400.16172665X-RAY DIFFRACTION99
3.9133-4.30640.17191380.16032632X-RAY DIFFRACTION99
4.3064-4.9280.15691410.15052666X-RAY DIFFRACTION99
4.928-6.2030.23831400.19492671X-RAY DIFFRACTION99
6.203-34.69270.20871370.18952605X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 15.1614 Å / Origin y: -20.6284 Å / Origin z: 27.6962 Å
111213212223313233
T0.0441 Å20.0041 Å20.0048 Å2-0.0481 Å20.0098 Å2--0.0507 Å2
L0.0566 °20.0465 °20.0528 °2-0.1297 °20.1193 °2--0.1485 °2
S0.0167 Å °-0.0117 Å °-0.0141 Å °-0.0351 Å °-0.0065 Å °-0.0413 Å °-0.023 Å °-0.0081 Å °0 Å °
Refinement TLS groupSelection details: all

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