[English] 日本語
Yorodumi
- PDB-2max: NMR structure of the RNA polymerase alpha subunit C-terminal doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2max
TitleNMR structure of the RNA polymerase alpha subunit C-terminal domain from Helicobacter pylori
ComponentsDNA-directed RNA polymerase subunit alphaPolymerase
KeywordsTRANSFERASE / RNA polymerase alpha subunit / HP1293 / JHP1213 / RPOA / DNA-directed RNA polymerase / nucleotidyltransferase / transcription
Function / homology
Function and homology information


DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / DNA binding
Similarity search - Function
RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsBorin, B.N. / Krezel, A.M.
CitationJournal: Protein Sci. / Year: 2014
Title: Helicobacter pylori RNA polymerase alpha-subunit C-terminal domain shows features unique to -proteobacteria and binds NikR/DNA complexes.
Authors: Borin, B.N. / Tang, W. / Krezel, A.M.
History
DepositionJul 21, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)14,1601
Polymers14,1601
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)15 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 14159.904 Da / Num. of mol.: 1 / Fragment: RNA Polymerase alpha subunit C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: jhp_1213, rpoA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9ZJT5, DNA-directed RNA polymerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCANH
1323D C(CO)NH
1423D H(CCO)NH
1523D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] RNAP alpha subunit CTD, 25 mM potassium phosphate, 225 mM potassium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] RNAP alpha subunit CTD, 25 mM potassium phosphate, 225 mM potassium chloride, 1 mM TCEP, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNAP alpha subunit CTD-1[U-15N]1
25 mMpotassium phosphate-21
225 mMpotassium chloride-31
1 mMTCEP-41
1 mMRNAP alpha subunit CTD-5[U-13C; U-15N]2
25 mMpotassium phosphate-62
225 mMpotassium chloride-72
1 mMTCEP-82
Sample conditionspH: 7.3 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

-
Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospinprocessing
SPARKYGoddardchemical shift assignment
SPARKYGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ProcheckNMRLaskowski and MacArthurgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 15

+
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