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- PDB-7g83: ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in c... -

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Basic information

Entry
Database: PDB / ID: 7g83
TitleARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z108545814
Components
  • Rho guanine nucleotide exchange factor 2
  • Transforming protein RhoA
KeywordsCYTOSOLIC PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
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 / 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 / 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 / forebrain radial glial cell differentiation / negative regulation of microtubule depolymerization / cell junction assembly / apical junction assembly / regulation of Rho protein signal transduction / 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 / negative regulation of necroptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / negative regulation of oxidative phosphorylation / cellular hyperosmotic response / 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 / regulation of small GTPase mediated signal transduction / 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 / NRAGE signals death through JNK / RHOB GTPase cycle / 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 / bicellular tight junction / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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)
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 / 3-propanamido-1-benzofuran-2-carboxamide / Transforming protein RhoA / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.31 Å
AuthorsBradshaw, W.J. / Katis, V.L. / 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: ARHGEF2 PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E.
History
DepositionJun 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)50,99122
Polymers49,5702
Non-polymers1,42120
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-9 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.353, 71.353, 196.765
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-704-

HOH

21B-868-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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 / Production host: Escherichia coli (E. coli) / 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 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92974

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Non-polymers , 4 types, 467 molecules

#3: Chemical ChemComp-YX2 / 3-propanamido-1-benzofuran-2-carboxamide


Mass: 232.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.31 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris, 2.6M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.31→67.1 Å / Num. obs: 106753 / % possible obs: 87.3 % / Redundancy: 23.4 % / Biso Wilson estimate: 19.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.02 / Rrim(I) all: 0.101 / Net I/σ(I): 16.9 / Num. measured all: 2492949 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.31-1.3312.23.8833023124680.3831.1284.0520.640.3
7.06-67.121.70.044206469500.9990.010.04574.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (17-FEB-2023)refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BNT

8bnt


Resolution: 1.31→18.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.059 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 5279 4.96 %RANDOM
Rwork0.1855 ---
obs0.1865 106358 86.8 %-
Displacement parametersBiso max: 130.23 Å2 / Biso mean: 25 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.6653 Å20 Å20 Å2
2---1.6653 Å20 Å2
3---3.3307 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.31→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 92 451 3970
Biso mean--38.59 35.94 -
Num. residues----424
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1460SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes690HARMONIC5
X-RAY DIFFRACTIONt_it3842HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion493SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3812SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3842HARMONIC20.012
X-RAY DIFFRACTIONt_angle_deg5210HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion14.38
LS refinement shellResolution: 1.31→1.33 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3258 123 5.78 %
Rwork0.3142 2005 -
all-2128 -
obs--37.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4805-0.19160.85750.0854-0.22681.277-0.0251-0.01690.0422-0.0334-0.0199-0.0093-0.0560.04520.045-0.0066-0.0116-0.0021-0.0232-0.0014-0.00310.4549-29.680810.9977
20.2094-0.0903-0.0420.26230.16110.3219-0.0141-0.0055-0.01840.00640.0393-0.00250.00890.0288-0.0251-0.0176-0.0077-0.0034-0.0079-0.00460.003615.4442-41.408232.6192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 181
2X-RAY DIFFRACTION2{ B|* }B204 - 448

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