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- PDB-5i6j: Crystal Structure of SRGAP2 F-BARx -

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Basic information

Entry
Database: PDB / ID: 5i6j
TitleCrystal Structure of SRGAP2 F-BARx
ComponentsSLIT-ROBO Rho GTPase-activating protein 2
KeywordsSIGNALING PROTEIN / SRGAP2 / F-BAR / Fx
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 / actin filament severing / filopodium assembly / regulation of small GTPase mediated signal transduction / inhibitory synapse assembly ...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 / actin filament severing / filopodium assembly / regulation of small GTPase mediated signal transduction / inhibitory synapse assembly / RHOF GTPase cycle / dendritic spine head / regulation of synapse assembly / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / positive regulation of GTPase activity / RAC3 GTPase cycle / neuron projection morphogenesis / phagocytic vesicle / RAC1 GTPase cycle / substrate adhesion-dependent cell spreading / GTPase activator activity / negative regulation of cell migration / RHO GTPases Activate Formins / small GTPase binding / lamellipodium / postsynaptic membrane / postsynaptic density / glutamatergic synapse / signal transduction / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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
SLIT-ROBO Rho GTPase-activating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Mol. Biol. Evol. / Year: 2017
Title: Structural History of Human SRGAP2 Proteins.
Authors: Sporny, M. / Guez-Haddad, J. / Kreusch, A. / Shakartzi, S. / Neznansky, A. / Cross, A. / Isupov, M.N. / Qualmann, B. / Kessels, M.M. / Opatowsky, Y.
History
DepositionFeb 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 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


Theoretical massNumber of molelcules
Total (without water)56,5551
Polymers56,5551
Non-polymers00
Water34219
1
A: SLIT-ROBO Rho GTPase-activating protein 2

A: SLIT-ROBO Rho GTPase-activating protein 2


Theoretical massNumber of molelcules
Total (without water)113,1102
Polymers113,1102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17360 Å2
ΔGint-111 kcal/mol
Surface area43970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.170, 29.900, 94.730
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number5
Space group name H-MC121

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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: 56555.230 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: O75044
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.55 Å3/Da / Density % sol: 51.69 % / Description: Thin plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: F-BARx-WT was eluted from the anion exchange column (MonoQ-GL10/100, GE Healthcare) in buffer containing 5% Glycerol, 25 mM Tris buffer pH=7.4, 5 mM ?-mercaptoethanol, and ~0.16 M NaCl at ...Details: F-BARx-WT was eluted from the anion exchange column (MonoQ-GL10/100, GE Healthcare) in buffer containing 5% Glycerol, 25 mM Tris buffer pH=7.4, 5 mM ?-mercaptoethanol, and ~0.16 M NaCl at the elution peak and concentrated to 18 mg/ml. F-BARx-WT crystals grew in 0.2 M ammonium citrate tribasic pH=7.25, 35% PEG1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.7→47.36 Å / Num. obs: 16087 / % possible obs: 98.6 % / Redundancy: 3.3 % / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREP11phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→101.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 19.058 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 0.777 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26275 800 5 %RANDOM
Rwork0.20349 ---
obs0.20661 15318 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.05 Å2
Baniso -1Baniso -2Baniso -3
1-8.23 Å20 Å2-3.78 Å2
2---1.76 Å20 Å2
3----6.21 Å2
Refinement stepCycle: 1 / Resolution: 2.7→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 19 3377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.974576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.00825.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.12815702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6241519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022517
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_it5.9077.5881640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.1111.3582044
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8768.2311769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.82413396
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 57 -
Rwork0.396 1087 -
obs--97.86 %

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