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- PDB-1tz1: Solution structure of the PB1 domain of CDC24P (short form) -

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Basic information

Entry
Database: PDB / ID: 1tz1
TitleSolution structure of the PB1 domain of CDC24P (short form)
ComponentsCell division control protein 24
KeywordsSIGNALING PROTEIN / PB1 domain / PCCR / PC motif / OPCA motif / yeast / cell polarity / protein-protein interaction
Function / homology
Function and homology information


regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / septin ring organization / protein localization to cell cortex / division septum / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip ...regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / septin ring organization / protein localization to cell cortex / division septum / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / regulation of exit from mitosis / cellular bud neck / regulation of Rho protein signal transduction / mating projection tip / establishment of cell polarity / guanyl-nucleotide exchange factor activity / cell cortex / intracellular signal transduction / nucleus / cytoplasm
Similarity search - Function
Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PB1 domain profile. / PB1 domain / Calponin homology domain ...Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PB1 domain profile. / PB1 domain / Calponin homology domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsYoshinaga, S. / Terasawa, H. / Ogura, K. / Noda, Y. / Ito, T. / Sumimoto, H. / Inagaki, F.
CitationJournal: To be Published
Title: Solution structure of the PB1 domain of CDC24P (short form)
Authors: Yoshinaga, S. / Terasawa, H. / Ogura, K. / Noda, Y. / Ito, T. / Sumimoto, H. / Inagaki, F.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 24


Theoretical massNumber of molelcules
Total (without water)9,1601
Polymers9,1601
Non-polymers00
Water0
1


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

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Components

#1: Protein Cell division control protein 24 / Calcium regulatory protein


Mass: 9160.293 Da / Num. of mol.: 1 / Fragment: PB1 Domain (Short Form)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Cdc24p / Plasmid: pPROEX-HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11433

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY, 3D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 or 2mM Cdc24p PB1 U-15N, 13C; 50mM potassium phosphate buffer; 150mM sodium chloride; 1mM sodium azide; 90% H2O, 10% D2O90% H2O/10% D2O
21 or 2mM Cdc24p PB1 U-15N, 13C; 50mM potassium phosphate buffer; 150mM sodium chloride; 1mM sodium azide; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM potassium phosphate buffer; 150mM sodium chloride
pH: 6.3 / Pressure: ambient / Temperature: 298 K

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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
NameDeveloperClassification
VNMRcollection
NMRPipeprocessing
Oliviadata analysis
ARIAstructure solution
ARIAJ.P.LINGE, S.I.O'DONOGHUE, M.NILGESrefinement
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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