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- PDB-2rqv: Solution structure of SH3CI domain of Bem1p -

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Basic information

Entry
Database: PDB / ID: 2rqv
TitleSolution structure of SH3CI domain of Bem1p
ComponentsBud emergence protein 1
KeywordsSIGNALING PROTEIN / Bem1p / SH3 / Cdc42p / Cytoplasm / Cytoskeleton / SH3 domain
Function / homology
Function and homology information


RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / PAR polarity complex / site of polarized growth / superoxide-generating NADPH oxidase activator activity / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location ...RHO GTPases Activate NADPH Oxidases / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / PAR polarity complex / site of polarized growth / superoxide-generating NADPH oxidase activator activity / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location / cellular bud neck / mating projection tip / regulation of Rho protein signal transduction / phosphatidylinositol-3-phosphate binding / superoxide anion generation / protein-macromolecule adaptor activity / cell cortex / molecular adaptor activity / cytoskeleton / mitochondrion / cytoplasm
Similarity search - Function
Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology ...Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / PB1 domain / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Bud emergence protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTakaku, T. / Ogura, K. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Solution structure of a novel Cdc42-binding module of Bem1 and its interaction with Ste20 and Cdc42
Authors: Takaku, T. / Ogura, K. / Kumeta, H. / Yoshida, N. / Inagaki, F.
History
DepositionDec 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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)11,6821
Polymers11,6821
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 / Bem1p / Suppressor of RHO3 protein 1


Mass: 11682.266 Da / Num. of mol.: 1 / Fragment: SH3CI domain, residues 156-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P29366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5mM [U-99% 13C; U-99% 15N] protein; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: 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 / Representative conformer: 1

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