[English] 日本語
Yorodumi
- PDB-2ahq: Solution Structure of the C-terminal RpoN Domain of Sigma-54 from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ahq
TitleSolution Structure of the C-terminal RpoN Domain of Sigma-54 from Aquifex aeolicus
ComponentsRNA polymerase sigma factor RpoN
KeywordsTRANSCRIPTION / Sigma-54 / sigma factors / solution structure / RNA polymerase
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / DNA-templated transcription, initiation / DNA binding
RNA polymerase sigma factor 54 / 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.
RNA polymerase sigma factor RpoN
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDoucleff, M. / Malak, L.T. / Pelton, J.G. / Wemmer, D.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70.
Authors: Doucleff, M. / Malak, L.T. / Pelton, J.G. / Wemmer, D.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)8,9661
Polymers8,9661
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150target function
RepresentativeModel #1lowest dyana target function

-
Components

#1: Protein/peptide RNA polymerase sigma factor RpoN / SIGMA-54


Mass: 8966.376 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpoN / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (BL21 (DE3) with pLysS) / References: UniProt: O66858

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1

Experiment-IDSolution-IDType
113D 15N-separated NOESY
213D N15-seperated TOCSY
32HNCA-J
42(H)CCH-TOCSY
523D 13C-separated NOESY
642D C13-HSQC
NMR detailsText: Other experiments performed and used for chemical shift assignments and obtaining restraints: CBCA(CO)NH, DQF-COSY, CC(CO)NH, H/D Exchange via N15-HSQC, HNHA - J couplings

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM Sigma-54 U-15N; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
20.8 mM Sigma-54 U-15N U-13C; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
30.8 mM Sigma-54 U-15; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 5% H20; 95% D205% H20; 95% D20
40.8 mM Sigma-54 U-15N U-10% 13C; 50 mM Hepes; 250 mM NaCl; 1 mM EDTA; 90% H20; 10% D2090% H20; 10% D20
Sample conditionsIonic strength: 50 mM Hepes; 250 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et al. (1995)processing
NMRView5.0.4Johnson & Blevins (1994)data analysis
DYANA1.5Guntert et al. (1997)structure solution
DYANA1.5Guntert et al. (1997)refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structures are based on a total 1064 restraints: 956 distance and 108 dihedral angle
NMR representativeSelection criteria: lowest dyana target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 150 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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