[English] 日本語
Yorodumi
- PDB-1ef4: SOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ef4
TitleSOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsDNA-DIRECTED RNA POLYMERASEPolymerase
KeywordsTRANSFERASE / THREE HELIX BUNDLE / ZINC BINDING / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, DNA-templated / DNA binding / zinc ion binding
Similarity search - Function
RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit N
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / DISTANCE GEOMETRY WITH SIMULATED ANNEALING
AuthorsMackereth, C.D. / Arrowsmith, C.H. / Edwards, A.M. / Mcintosh, L.P. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
Authors: Mackereth, C.D. / Arrowsmith, C.H. / Edwards, A.M. / McIntosh, L.P.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5102
Polymers6,4441
Non-polymers651
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with acceptable covalent geometry
RepresentativeModel #1

-
Components

#1: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase / SUBUNIT N


Mass: 6444.494 Da / Num. of mol.: 1 / Fragment: SUBUNIT RPB10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: O26147, DNA-directed RNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D METHYL-METHYL 13C SEPARATED NOESY
1212D NOESY
1313D 13C-SEPARATED NOESY
1413D 15N-SEPARATED NOESY
151HNHA
1612D CT-HMQC-J
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: 0.5MM RPB10 U-15N,13C 20MM DEUTERATED D-TRIS; 0.15M NACL; 2MM BETA- MERCAPTOETHANOL; 99% D2O, 1% H2O
Sample conditionsIonic strength: 150mM_NACL / pH: 7.50 / Pressure: AMBIENT / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR 3.851, ARIA1999BRUNGER (X-PLOR), NILGES (ARIA)refinement
VNMR6structure solution
FELIX95structure solution
RefinementMethod: DISTANCE GEOMETRY WITH SIMULATED ANNEALING / Software ordinal: 1
Details: REFINED USING ARIA AMBIGUOUS AND UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9,43,44 WITH IDEALIZED ...Details: REFINED USING ARIA AMBIGUOUS AND UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9,43,44 WITH IDEALIZED TETRAHEDRAL RESTRAINTS WERE ADDED IN THE FINAL ROUNDS OF REFINEMENT; THE COORDINATING LIGANDS AND THEIR GEOMETRIC ARRANGEMENT WERE IDENTIFIED BASED ON INITIAL NOE-DERIVED STRUCTURES CALCULATED WITHOUT INCLUSION OF THE METAL ION. THREE N- TERMINAL RESIDUES (GLY-SER-HIS) REMAINING FROM CLEAVAGE OF THE HIS-TAG WERE DISORDERED AND NOT INCLUDED IN THE FINAL ENSEMBLE.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 60 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
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

+
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

-
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