[English] 日本語
Yorodumi
- PDB-2rp5: Solution structure of the oligomerization domain in CEP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rp5
TitleSolution structure of the oligomerization domain in CEP-1
ComponentsPutative uncharacterized protein cep-1
KeywordsTRANSCRIPTION / CEP-1 / p53 / Oligomerization domain / SAM domain
Function / homology
Function and homology information


meiotic chromosome segregation / response to starvation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / transcription repressor complex / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / response to oxidative stress / sequence-specific DNA binding / response to hypoxia ...meiotic chromosome segregation / response to starvation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / transcription repressor complex / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / response to oxidative stress / sequence-specific DNA binding / response to hypoxia / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA polymerase; domain 1 - #830 / Transcription factor CEP-1, DNA-binding domain / CEP-1, DNA binding / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor cep-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsOu, H.D. / Doetsch, V.
CitationJournal: Embo J. / Year: 2007
Title: Structural evolution of C-terminal domains in the p53 family
Authors: Ou, H.D. / Loehr, F. / Vogel, V. / Maentele, W. / Doetsch, V.
History
DepositionMay 1, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein cep-1
B: Putative uncharacterized protein cep-1


Theoretical massNumber of molelcules
Total (without water)31,3422
Polymers31,3422
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

-
Components

#1: Protein Putative uncharacterized protein cep-1 / Transcription factor CEP-1


Mass: 15670.919 Da / Num. of mol.: 2
Fragment: Oligomerization domain of CEP-1, UNP residues 514-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cep-1, F52B5.5, F52B5.5a / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q20646

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1243D HNCA
1313D 1H-15N NOESY
1443D 1H-13C NOESY
1532D 1H-1H NOESY
1624D J Resolve NOESY
1743D HN(CO)CA

-
Sample preparation

Details
Solution-IDContentsSolvent system
120mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.4-0.6 mM [U-15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
220mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5mM [U-13C; U-15N] protein, 100% D2O100% D2O
320mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.4-0.6mM protein, 100% D2O100% D2O
420mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.4-0.6mM [U-13C; U-15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
100 mMsodium chloride1
0.03 %sodium azide1
0.4 mMprotein[U-15N]1
20 mMsodium phosphate2
100 mMsodium chloride2
0.03 %sodium azide2
0.5 mMprotein[U-13C; U-15N]2
20 mMsodium phosphate3
100 mMsodium chloride3
0.03 %sodium azide3
0.4 mMprotein3
20 mMsodium phosphate4
100 mMsodium chloride4
0.03 %sodium azide4
0.4 mMprotein[U-13C; U-15N]4
Sample conditionspH: 7 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue, Nilgeschemical shift assignment
ARIA1.2Linge, O'Donoghue, Nilgesrefinement
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio, Baxgeometry optimization
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 100 structures were calculated, and the best 20 lowest energies structures underwent water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

+
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://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