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- PDB-5i6r: Crystal Structure of srGAP2 F-BARx WT Form-1 -

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Basic information

Entry
Database: PDB / ID: 5i6r
TitleCrystal Structure of srGAP2 F-BARx WT Form-1
ComponentsSLIT-ROBO Rho GTPase-activating protein 2
KeywordsSIGNALING PROTEIN / srGAP2 / F-BAR / CAKUT / C280Y
Function / homology
Function and homology information


lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / dendritic spine development / inhibitory synapse assembly / actin filament severing / filopodium assembly / RHOF GTPase cycle ...lamellipodium assembly involved in ameboidal cell migration / extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration / excitatory synapse assembly / negative regulation of neuron migration / Inactivation of CDC42 and RAC1 / dendritic spine development / inhibitory synapse assembly / actin filament severing / filopodium assembly / RHOF GTPase cycle / regulation of small GTPase mediated signal transduction / dendritic spine head / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / RAC3 GTPase cycle / phagocytic vesicle / RAC1 GTPase cycle / GTPase activator activity / substrate adhesion-dependent cell spreading / neuron projection morphogenesis / positive regulation of GTPase activity / negative regulation of cell migration / RHO GTPases Activate Formins / small GTPase binding / lamellipodium / postsynaptic membrane / postsynaptic density / signal transduction / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
srGAP1/2/3, SH3 domain / : / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain ...srGAP1/2/3, SH3 domain / : / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
ACETATE ION / D-MALATE / TRIETHYLENE GLYCOL / SLIT-ROBO Rho GTPase-activating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSporny, M. / Guez-Haddad, J. / Isupov, M.N. / Opatowsky, Y.
Funding support Israel, 2items
OrganizationGrant numberCountry
ISF182/10 and 1425/15 Israel
BSF2013310 Israel
CitationJournal: To Be Published
Title: Structural Basis for srGAP2 Membrane Interactions, and Antagonism by the Human Specific Paralog srGAP2C
Authors: Sporny, M. / Guez-Haddad, J. / Isupov, M.N. / Opatowsky, Y.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0185
Polymers56,6151
Non-polymers4024
Water4,540252
1
A: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules

A: SLIT-ROBO Rho GTPase-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,03510
Polymers113,2312
Non-polymers8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19810 Å2
ΔGint-111 kcal/mol
Surface area43280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.300, 29.760, 94.630
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein SLIT-ROBO Rho GTPase-activating protein 2 / srGAP2 / Formin-binding protein 2 / Rho GTPase-activating protein 34


Mass: 56615.262 Da / Num. of mol.: 1 / Mutation: C280Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRGAP2, ARHGAP34, FNBP2, KIAA0456, SRGAP2A / Plasmid: pHis Parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O75044
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: F-BARx-C280Y was eluted in 25 mM phosphate buffer pH 8, 120 mM NaCl, 1 mM DTT, concentrated to 12 mg/ml, and crystallized in 5% v/v Tacsimate pH=5.5, 12% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.15→94.5 Å / Num. obs: 28948 / % possible obs: 99.42 % / Redundancy: 3.8 % / Net I/σ(I): 11.12

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→94.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.215
RfactorNum. reflection% reflectionSelection details
Rfree0.26013 1320 4.6 %RANDOM
Rwork0.20299 ---
obs0.20562 27627 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.881 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å20 Å2-1.95 Å2
2--0.56 Å20 Å2
3---2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.15→94.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 0 27 252 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9755072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6395485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63125.502209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71615798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5271527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022835
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1274.1831746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4236.2322191
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.854.4392008
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.45838.54715455
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 92 -
Rwork0.316 1967 -
obs--99.37 %

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