[English] 日本語
Yorodumi
- PDB-1pqs: Solution structure of the C-terminal OPCA domain of yCdc24p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pqs
TitleSolution structure of the C-terminal OPCA domain of yCdc24p
ComponentsCell division control protein 24
KeywordsCELL CYCLE / Alpha and Beta protein
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 / mating projection tip / regulation of Rho protein signal transduction / 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 / 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. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) 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
AuthorsLeitner, D. / Wahl, M. / Labudde, D. / Diehl, A. / Schmieder, P. / Pires, J.R. / Fossi, M. / Leidert, M. / Krause, G. / Oschkinat, H.
CitationJournal: Febs Lett. / Year: 2005
Title: The solution structure of an N-terminally truncated version of the yeast CDC24p PB1 domain shows a different beta-sheet topology.
Authors: Leitner, D. / Wahl, M. / Labudde, D. / Krause, G. / Diehl, A. / Schmieder, P. / Pires, J.R. / Fossi, M. / Wiedemann, U. / Leidert, M. / Oschkinat, H.
History
DepositionJun 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell division control protein 24


Theoretical massNumber of molelcules
Total (without water)8,9731
Polymers8,9731
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
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cell division control protein 24


Mass: 8973.029 Da / Num. of mol.: 1 / Fragment: C-terminal OPCA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Cdc24p / Plasmid: pet17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P11433

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 15N-separated NOESY
1214D 13C/15N-separated NOESY
1313D 13C-separated NOESY
2423D 15N-separated NOESY
NMR detailsText: the structures are based on a total of 1754 restraints, 1615 are NOE-derived distance constraints, 75 dihedral angle restraints, 64 distance restraints from hydrogen bonds.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM OPCA U-15N, 13C; 20mM POTASSIUM PHOSPHATE BUFFER, 50mM NACL, 0.02% SODIUM AZID; pH 6.093% H2O/7% D2O
21.4mM OPCA U-15N; 20mM POTASSIUM PHOSPHATE BUFFER, 50mM NACL, 0.02% SODIUM AZID; pH 6.093% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM POTASSIUM PHOSPHATE BUFFER, 50mM SODIUM CHLORIDE 6.0 ambient 299.6 K
220mM POTASSIUM PHOSPHATE, 50mM SODIUM CHLORIDE 6.0 ambient 299.6 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
PASTE/PAPST1Labudde et al.collection
XwinNMR2.6processing
NMRPipeDelaglio et al.processing
Sparky3.1Goddard et al.data analysis
CATCH231.5Croft et al.data analysis
PLATON1Labudde et al.data analysis
ARIA/CNS1.2Linge et al.structure solution
ARIA/CNS1.2Linge et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more