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- PDB-7g84: ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in c... -

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Basic information

Entry
Database: PDB / ID: 7g84
TitleARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1102357527
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 / 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 / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / establishment of epithelial cell apical/basal polarity / beta selection / 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 / PCP/CE pathway / positive regulation of podosome assembly / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / regulation of small GTPase mediated signal transduction / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / odontogenesis / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / 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 / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / endothelial cell migration / RHOA GTPase cycle / mitotic spindle assembly / 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 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / secretory granule membrane / small monomeric GTPase / guanyl-nucleotide exchange factor activity / 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 / Chem-YX6 / 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: 1.811 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)50,61418
Polymers49,5702
Non-polymers1,04416
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-8 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.342, 71.342, 196.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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, 420 molecules

#3: Chemical ChemComp-YX6 / N-[(3R)-6-oxopiperidin-3-yl]-1,3-thiazole-4-carboxamide


Mass: 225.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3O2S / 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.: 11 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.52 Å3/Da / Density % sol: 51.25 % / 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: 1.81→35.68 Å / Num. obs: 47328 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 25.16 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.101 / Rrim(I) all: 0.354 / Net I/σ(I): 6.7 / Num. measured all: 564576 / 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
1.81-1.8511.83.2593258127500.4350.9753.4040.7100
9.06-35.688.60.06740564730.9910.0230.07133.998.8

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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: 1.811→26.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2334 4.95 %RANDOM
Rwork0.1945 ---
obs0.1963 47171 99.9 %-
Displacement parametersBiso max: 78.23 Å2 / Biso mean: 27.16 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.7675 Å20 Å20 Å2
2---3.7675 Å20 Å2
3---7.5351 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.811→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 64 406 3897
Biso mean--39.31 36.87 -
Num. residues----424
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1456SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes684HARMONIC5
X-RAY DIFFRACTIONt_it3807HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion492SEMIHARMONIC5
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_contact3425SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3807HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5165HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion15.28
LS refinement shellResolution: 1.81→1.82 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3837 43 4.56 %
Rwork0.3243 901 -
all-944 -
obs--99.67 %
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)
10.6184-0.32840.90530.2016-0.37211.7048-0.04-0.00860.0398-0.0195-0.0021-0.0275-0.07480.05910.0421-0.0307-0.0214-0.0055-0.0453-0.00570.00549.9706-29.631611.2745
20.1781-0.0675-0.02640.30010.14820.4032-0.009-0.0113-0.0276-0.00120.0269-0.00960.0040.0181-0.0179-0.035-0.0078-0.0026-0.0178-0.00080.019815.4848-41.345432.5717
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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