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- PDB-2czo: Solution Structure of the PX Domain of Bem1p -

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Basic information

Entry
Database: PDB / ID: 2czo
TitleSolution Structure of the PX Domain of Bem1p
ComponentsBud emergence protein 1
KeywordsSIGNALING PROTEIN / PX DOMAIN / BEM1P / PHOSPHOINOSITIDE BINDING
Function / homology
Function and homology information


positive regulation of vacuole fusion, non-autophagic / RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / site of polarized growth / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location ...positive regulation of vacuole fusion, non-autophagic / RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / site of polarized growth / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location / cellular bud neck / regulation of Rho protein signal transduction / mating projection tip / phosphatidylinositol-3-phosphate binding / cell cortex / protein-macromolecule adaptor activity / molecular adaptor activity / cytoskeleton / mitochondrion / cytoplasm
Similarity search - Function
Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / Phox-like domain / PX Domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / Phox-like domain / PX Domain / PB1 domain / PB1 domain / : / PB1 domain profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bud emergence protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsMaeda, A. / Ogura, K. / Horiuchi, M. / Kumeta, H. / Fujioka, Y. / Inagaki, F.
CitationJournal: To be Published
Title: Solution structure of the PX domain of Bem1p
Authors: Maeda, A. / Ogura, K. / Horiuchi, M. / Kumeta, H. / Fujioka, Y. / Inagaki, F.
History
DepositionJul 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bud emergence protein 1


Theoretical massNumber of molelcules
Total (without water)17,8051
Polymers17,8051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bud emergence protein 1 / Bem1 Protein


Mass: 17805.174 Da / Num. of mol.: 1 / Fragment: PX DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BEM1 / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM Bem1p PX domain U-15N, 13C; 20mM MES buffer; 200mM NaCl90% H2O/10% D2O
20.4mM Bem1p PX domain U-15N; 20mM MES buffer; 200mM NaCl90% H2O/10% D2O
Sample conditionsIonic strength: 200mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cWelchcollection
NMRPipe23Delaglioprocessing
Sparky3.11Goddarddata analysis
PACES1Zhoudata analysis
CYANA2Guntertstructure solution
CYANA2Guntertrefinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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