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- PDB-8bnt: The DH domain of ARHGEF2 bound to RhoA -

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Basic information

Entry
Database: PDB / ID: 8bnt
TitleThe DH domain of ARHGEF2 bound to RhoA
Components
  • Rho guanine nucleotide exchange factor 2
  • Transforming protein RhoA
KeywordsCYTOSOLIC PROTEIN / GTP / GDP / Guanine / cytoskeleton
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / 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 ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / 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 / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / cellular response to muramyl dipeptide / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / positive regulation of neuron migration / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / negative regulation of microtubule depolymerization / cell junction assembly / regulation of Rho protein signal transduction / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / negative regulation of cell size / negative regulation of necroptotic process / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / cellular hyperosmotic response / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / PCP/CE pathway / positive regulation of podosome assembly / regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / PI3K/AKT activation / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / odontogenesis / ossification involved in bone maturation / regulation of focal adhesion assembly / apical junction complex / negative chemotaxis / RHOB GTPase cycle / myosin binding / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / stress fiber assembly / regulation of neuron projection development / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / androgen receptor signaling pathway / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / endothelial cell migration / mitotic spindle assembly / RHOA GTPase cycle / negative regulation of cell-substrate adhesion / Rho protein signal transduction / membrane scission GTPase motor activity / positive regulation of T cell migration / bicellular tight junction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / substantia nigra development / EPHB-mediated forward signaling / substrate adhesion-dependent cell spreading / positive regulation of neuron differentiation / regulation of cell migration / secretory granule membrane / small monomeric GTPase / actin filament organization / guanyl-nucleotide exchange factor activity
Similarity search - Function
ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / Transforming protein RhoA / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Grosjean, H. / Bountra, C. / von Delft, F. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: To Be Published
Title: The DH domain of ARHGEF2 bound to RhoA
Authors: Bradshaw, W.J. / Katis, V.L. / Grosjean, H. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionNov 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Rho guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,65122
Polymers49,5702
Non-polymers1,08120
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-7 kcal/mol
Surface area20940 Å2
Unit cell
Length a, b, c (Å)71.432, 71.432, 196.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-505-

FMT

21B-872-

HOH

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Components

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


Mass: 20925.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61586, small monomeric GTPase
#2: Protein Rho guanine nucleotide exchange factor 2 / Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell ...Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell nucleolar antigen p40


Mass: 28644.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q92974
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.6 M sodium formate, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.4→71.43 Å / Num. obs: 101036 / % possible obs: 100 % / Redundancy: 45.8 % / CC1/2: 0.999 / Rpim(I) all: 0.072 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 22.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4914 / CC1/2: 0.403 / Rpim(I) all: 3.132 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D0N

4d0n


Resolution: 1.4→57.845 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.471 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1751 2000 1.982 %
Rwork0.1297 98884 -
all0.131 --
obs-100884 99.972 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.307 Å2-0 Å2-0 Å2
2--0.307 Å2-0 Å2
3----0.614 Å2
Refinement stepCycle: LAST / Resolution: 1.4→57.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 65 451 3943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123811
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163578
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6525163
X-RAY DIFFRACTIONr_angle_other_deg0.6091.5678412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.248532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24510742
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66510185
X-RAY DIFFRACTIONr_chiral_restr0.0910.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02737
X-RAY DIFFRACTIONr_nbd_refined0.2560.2652
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22966
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21735
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.222
X-RAY DIFFRACTIONr_nbd_other0.1710.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.237
X-RAY DIFFRACTIONr_mcbond_it2.9091.7411804
X-RAY DIFFRACTIONr_mcbond_other2.911.7421805
X-RAY DIFFRACTIONr_mcangle_it3.5472.6142270
X-RAY DIFFRACTIONr_mcangle_other3.5462.6162271
X-RAY DIFFRACTIONr_scbond_it5.7372.3652007
X-RAY DIFFRACTIONr_scbond_other5.6022.3391978
X-RAY DIFFRACTIONr_scangle_it6.0913.2892858
X-RAY DIFFRACTIONr_scangle_other6.0913.2892859
X-RAY DIFFRACTIONr_lrange_it5.51230.4024231
X-RAY DIFFRACTIONr_lrange_other5.45126.8044106
X-RAY DIFFRACTIONr_rigid_bond_restr5.1537389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.3061510.30971600.30873190.9140.91199.89070.312
1.436-1.4760.3151460.2670090.26171560.930.94699.9860.258
1.476-1.5180.2561320.21468570.21569910.9590.96699.97140.206
1.518-1.5650.2581380.19666290.19767680.9520.97199.98520.181
1.565-1.6160.1991200.16264490.16265700.9740.98199.98480.143
1.616-1.6730.1941340.14262390.14363780.9740.98699.92160.123
1.673-1.7360.1741280.12460370.12561670.980.98999.96760.105
1.736-1.8070.1511010.11258280.11359300.9870.99199.98310.094
1.807-1.8870.1831050.10655890.10756960.980.99299.96490.089
1.887-1.9790.1661380.10253360.10354740.9830.9931000.088
1.979-2.0860.12890.08950820.08951730.9910.99599.96130.078
2.086-2.2130.131030.08748500.08849530.9920.9961000.08
2.213-2.3650.125810.08845750.08946560.990.9951000.081
2.365-2.5540.152850.08942870.0943720.9870.9951000.083
2.554-2.7980.169840.11339360.11440200.9850.9921000.107
2.798-3.1270.165830.12535840.12636670.9840.991000.121
3.127-3.6090.158630.11832080.11932710.9820.9921000.118
3.609-4.4160.156480.11427390.11427870.9860.9921000.118
4.416-6.2260.204390.15521790.15622180.9840.9891000.162
6.226-57.8450.226320.21213110.21313450.9780.96999.85130.265

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