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- PDB-6lp3: Structural basis and functional analysis epo1-bem3p complex for b... -

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Basic information

Entry
Database: PDB / ID: 6lp3
TitleStructural basis and functional analysis epo1-bem3p complex for bud growth
Components
  • GTPase-activating protein BEM3
  • Uncharacterized protein YMR124W
KeywordsCELL ADHESION / Budding yeast / Organelle inheritance / Endoplasmic reticulum inheritance / Polarisome / Epo1p / Bem3p.
Function / homology
Function and homology information


endoplasmic reticulum polarization / : / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / septin ring organization / RHOA GTPase cycle / incipient cellular bud site ...endoplasmic reticulum polarization / : / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / septin ring organization / RHOA GTPase cycle / incipient cellular bud site / cellular bud tip / cellular bud neck / mating projection tip / phosphatidylinositol-3-phosphate binding / negative regulation of Rho protein signal transduction / establishment of cell polarity / regulation of GTPase activity / Neutrophil degranulation / GTPase activator activity / positive regulation of GTPase activity / cell cortex / signal transduction / cytoplasm
Similarity search - Function
PhoX homologous domain, present in p47phox and p40phox. / PX domain / Phox homology / PX 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 / PH domain ...PhoX homologous domain, present in p47phox and p40phox. / PX domain / Phox homology / PX 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
GTPase-activating protein BEM3 / Uncharacterized protein YMR124W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.547 Å
AuthorsWang, J. / Li, L. / Ming, Z.H. / Wu, L.J. / Yan, L.M.
CitationJournal: To Be Published
Title: Structural basis and functional analysis epo1-bem3p complex for bud growth
Authors: Wang, J.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YMR124W
B: Uncharacterized protein YMR124W
C: GTPase-activating protein BEM3
D: Uncharacterized protein YMR124W
E: Uncharacterized protein YMR124W
F: GTPase-activating protein BEM3


Theoretical massNumber of molelcules
Total (without water)112,3056
Polymers112,3056
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.405, 119.405, 144.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Uncharacterized protein YMR124W


Mass: 22375.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YMR124W, YM8564.06 / Production host: Escherichia coli (E. coli) / References: UniProt: P39523
#2: Protein GTPase-activating protein BEM3 / Bud emergence protein 3


Mass: 11400.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BEM3, YPL115C, LPH12C / Production host: Escherichia coli (E. coli) / References: UniProt: P32873

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M Ammonium sulfate, 0.1 M MES, pH 6.5, 10% 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.547→46.032 Å / Num. obs: 13161 / % possible obs: 99.9 % / Redundancy: 18 % / Rmerge(I) obs: 0.431 / Net I/σ(I): 10.31
Reflection shellResolution: 3.95→4.23 Å / Rmerge(I) obs: 0.961 / Num. unique obs: 1249

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 3.547→46.032 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.398 674 5.12 %
Rwork0.3397 12487 -
obs0.3427 13161 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 383.6 Å2 / Biso mean: 122.3199 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.547→46.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 0 0 4661
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.547-3.82020.41431160.3898243599
3.8202-4.20440.38291340.35062445100
4.2044-4.81230.41071510.34992468100
4.8123-6.06070.44921410.38832496100
6.0607-460.37191320.30192643100

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