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- PDB-8bux: Rab-binding domain of human MiniBAR -

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Basic information

Entry
Database: PDB / ID: 8bux
TitleRab-binding domain of human MiniBAR
ComponentsGranule associated Rac and RHOG effector protein 1
KeywordsPROTEIN TRANSPORT / Rac effector / Rab effector
Function / homology
Function and homology information


CCR4-NOT complex binding / Rac protein signal transduction / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / P-body / small GTPase binding / cytosol
Similarity search - Function
Domain of unknown function DUF4745 / Granule associated Rac and RHOG effector protein 1 / Domain of unknown function (DUF4745)
Similarity search - Domain/homology
MALONATE ION / Granule associated Rac and RHOG effector protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsPylypenko, O. / Hammich, H. / Houdusse, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE13-0024-02 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0016-02 France
CitationJournal: To Be Published
Title: MiniBAR/KIAA0355 is a dual Rac and Rab effector that controls actin contractility and trafficking for successful ciliogenesis
Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. ...Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. / Callebaut, I. / Formstecher, E. / Houdusse, A. / David, N. / Pylypenko, O. / Echard, A.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 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: Granule associated Rac and RHOG effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8915
Polymers36,6011
Non-polymers2904
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-2 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.388, 123.956, 38.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

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Components

#1: Protein Granule associated Rac and RHOG effector protein 1 / GARRE1


Mass: 36600.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GARRE1, KIAA0355 / Production host: Escherichia coli (E. coli) / References: UniProt: O15063
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


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

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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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.856→28.58 Å / Num. obs: 24856 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.06 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 1.856→1.888 Å / Num. unique obs: 4668 / CC1/2: 0.849

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
autoPROCdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→28.58 Å / SU ML: 0.1573 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 1210 4.87 %
Rwork0.1649 23639 -
obs0.1672 24849 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.67 Å2
Refinement stepCycle: LAST / Resolution: 1.86→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 19 252 2433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992257
X-RAY DIFFRACTIONf_angle_d1.05183067
X-RAY DIFFRACTIONf_chiral_restr0.0531359
X-RAY DIFFRACTIONf_plane_restr0.0064402
X-RAY DIFFRACTIONf_dihedral_angle_d13.1795837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.930.27311430.25192586X-RAY DIFFRACTION99.96
1.93-2.020.25991290.19622594X-RAY DIFFRACTION99.71
2.02-2.120.21191290.18022590X-RAY DIFFRACTION99.85
2.12-2.260.18061270.15662611X-RAY DIFFRACTION99.74
2.26-2.430.19231400.1552582X-RAY DIFFRACTION99.63
2.43-2.680.19391320.15972608X-RAY DIFFRACTION99.35
2.68-3.060.23121290.16152630X-RAY DIFFRACTION99.39
3.06-3.860.20431370.14432669X-RAY DIFFRACTION99.4
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)
10.4598477366480.1077369143-0.1241467379350.5473975078390.01170591579480.835550978808-0.07025227599630.04978796938290.0476535556431-0.1042026687480.0157535299023-0.00759850391019-0.0705784653638-0.04921558811511.98640061479E-50.1749218839380.0245763876581-0.01481503672890.1974967767710.01451704554130.20315478868649.556447232362.014416177749.3956921851
20.09670732899810.1019516942420.07675261777761.01215974170.4227236676220.2196789866220.0260444031930.00265136328135-0.07648436358180.08014926854120.0291194517891-0.2411924248270.174691574167-0.02993590691692.20121170877E-50.258690401183-0.0133230787881-0.005495078214750.2032185941370.01239563662130.22606367727148.790535278635.075763254647.4786351856
30.6261400988160.2668393255190.2489502894361.45894859211-0.07240337158020.233509513726-0.020347815577-0.0285471388077-0.0482754674804-0.100821420644-0.0428990998180.147439802340.0985297635997-0.236432567752-0.000415378202420.196506165594-0.0444037348680.008624285150920.2035148259860.004730222681560.18481830386141.844204556542.41477485845.8594009484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 220 through 312 )
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 426 )
3X-RAY DIFFRACTION3chain 'A' and (resid 427 through 543 )

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