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- PDB-1ip9: SOLUTION STRUCTURE OF THE PB1 DOMAIN OF BEM1P -

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Basic information

Entry
Database: PDB / ID: 1ip9
TitleSOLUTION STRUCTURE OF THE PB1 DOMAIN OF BEM1P
ComponentsBEM1 PROTEIN
KeywordsSIGNALING PROTEIN / ubiquitin alpha/beta roll
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 / phosphatidylinositol-3-phosphate binding / mating projection tip / 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 / : / PB1 domain / PB1 domain / : / PB1 domain profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Bud emergence protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / dynamical simulated annealing
AuthorsTerasawa, H. / Noda, Y. / Ito, T. / Hatanaka, H. / Ichikawa, S. / Ogura, K. / Sumimoto, H. / Inagaki, F.
Citation
Journal: EMBO J. / Year: 2001
Title: Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif.
Authors: Terasawa, H. / Noda, Y. / Ito, T. / Hatanaka, H. / Ichikawa, S. / Ogura, K. / Sumimoto, H. / Inagaki, F.
#1: Journal: Embo J. / Year: 2001
Title: Novel modular domain PB1 recognizes PC motif to mediate functional protein-protein interactions
Authors: Ito, T. / Matsui, Y. / Ago, T. / Ota, K. / Sumimoto, H.
History
DepositionApr 26, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4Dec 27, 2023Group: 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: BEM1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,5201
Polymers9,5201
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 / 200structures with the lowest energy
Representative

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Components

#1: Protein BEM1 PROTEIN


Mass: 9519.925 Da / Num. of mol.: 1 / Fragment: PB1 DOMAIN(RESIDUES 472-551)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PPROEX-HTA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P29366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
141HNHB
151HN(CO)HB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2mM Bem PB1 U-15N, 13C; 50mM potassium phosphate pH 6.3; 150mM sodium chloride; 1mM sodium azide; 90% H2O, 10% D2O
Solvent system: 90% H2O, 10% D2O, 100% D2O
Sample conditionsIonic strength: 50mM potassium phosphate, 150mM sodium chloride
pH: 6.3 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: dynamical simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1334 restraints, 1269 are NOE-derived distance constraints, 65 dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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