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- PDB-7g9b: ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in c... -

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Basic information

Entry
Database: PDB / ID: 7g9b
TitleARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102116-001
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


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 / regulation of osteoblast proliferation / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure ...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 / regulation of osteoblast proliferation / 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 / 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 / ossification involved in bone maturation / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / myosin binding / 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 / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / endothelial cell migration / mitotic spindle assembly / RHOA GTPase cycle / positive regulation of T cell migration / regulation of microtubule cytoskeleton organization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / substantia nigra development / EPHB-mediated forward signaling / positive regulation of neuron differentiation / regulation of cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / kidney development / small monomeric GTPase / secretory granule membrane / G protein activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / neuron migration / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / VEGFA-VEGFR2 Pathway / cytoplasmic side of plasma membrane / ruffle 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
FORMIC ACID / N-(3-methylphenyl)acetamide / Transforming protein RhoA / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.553 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

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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)50,19812
Polymers49,5702
Non-polymers62810
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-7 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.802, 70.802, 195.820
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, 240 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ZG0 / N-(3-methylphenyl)acetamide


Mass: 149.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.48 Å3/Da / Density % sol: 50.31 % / Mosaicity: 0.17 °
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: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.55→66.58 Å / Num. obs: 17061 / % possible obs: 100 % / Redundancy: 16.9 % / Biso Wilson estimate: 60.9 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 1.107 / Rpim(I) all: 0.27 / Rrim(I) all: 1.14 / Net I/σ(I): 4.9 / Num. measured all: 287818 / Scaling rejects: 209
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obsRmerge(I) obs
2.55-2.6917.74275424120.3964.24718.2870.7
8.07-66.581385056560.9970.0250.09516.80.091

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (17-FEB-2023)refinement
Aimless0.7.9data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BNT

8bnt


Resolution: 2.553→24 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.761 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.254 / SU Rfree Blow DPI: 0.373 / SU Rfree Cruickshank DPI: 0.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 858 5.1 %RANDOM
Rwork0.2058 ---
obs0.2104 16815 99.1 %-
Displacement parametersBiso max: 114.89 Å2 / Biso mean: 62.63 Å2 / Biso min: 15.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.2798 Å20 Å20 Å2
2---2.2798 Å20 Å2
3---4.5596 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.553→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 40 231 3612
Biso mean--66.01 50.91 -
Num. residues----414
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1376SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes643HARMONIC5
X-RAY DIFFRACTIONt_it3611HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
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_contact2915SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3611HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg4896HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion19.35
LS refinement shellResolution: 2.55→2.58 Å / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.3628 16 3.99 %
Rwork0.3169 385 -
all-401 -
obs--90.83 %
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)
10.4945-0.43910.76641.056-1.02183.3179-0.09790.0356-0.0670.04150.08280.0675-0.20620.11940.01510.0822-0.0603-0.00170.11690.031-0.321110.4272-29.066710.9529
20.2582-0.1001-0.09390.1872-0.41811.7727-0.0327-0.0556-0.08170.02890.03230.0697-0.0870.25250.00050.0791-0.0127-0.00670.1060.0127-0.26314.974-39.263233.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 181
2X-RAY DIFFRACTION2{ B|* }B204 - 438

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