[English] 日本語
Yorodumi
- PDB-2o8k: NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o8k
TitleNMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Components
  • 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
  • RNA polymerase sigma factor RpoN
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HELIX-TURN-HELIX / TRANSCRIPTION FACTOR / SIGMA-54 / RNA POLYMERASE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / DNA-templated transcription initiation / DNA binding
Similarity search - Function
RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / Sigma-54 factors family profile. / RNA polymerase sigma factor 54 / Homeodomain-like ...RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / Sigma-54 factors family profile. / RNA polymerase sigma factor 54 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor RpoN
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / docking, rigid-body minimization, simulated annealing
AuthorsDoucleff, M. / Pelton, J.G. / Lee, P.S. / Wemmer, D.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis of DNA recognition by the alternative sigma-factor, sigma54.
Authors: Doucleff, M. / Pelton, J.G. / Lee, P.S. / Nixon, B.T. / Wemmer, D.E.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
C: 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
A: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)16,0483
Polymers16,0483
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 / 5020 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively
RepresentativeModel #1lowest energy

-
Components

#1: DNA chain 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'


Mass: 4252.761 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'


Mass: 4306.846 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein RNA polymerase sigma factor RpoN


Mass: 7488.800 Da / Num. of mol.: 1 / Fragment: C-TERMINAL RPON DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpoN / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) with Rosetta.pLysS plasmid
References: UniProt: O66858

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D C13-seperated[F1], C12-filtered[F2] NOESY
2223D C13-seperated NOESY
3333D 15N-seperated NOESY
1412D C12-filtered[F1,F2] NOESY
1512D C12-filtered[F1] NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O
21 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
31 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM NaCl 6.9ambient 303 K
2250 mM NaCl 6.9ambient 303 K
3250 mM NaCl 6.9ambient 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et al. 1995processing
NMRView5.0.4Johnson et al. 1994data analysis
CYANA2.1Guntert 2004structure solution
X-PLOR2.14Schwieters et al. 2003refinement
RefinementMethod: docking, rigid-body minimization, simulated annealing
Software ordinal: 1
Details: protein and DNA structures determined individually via simulated annealing; the two structures were docked using rigid body minimization; the whole structure was refined by simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively
Conformers calculated total number: 50 / 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://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