[English] 日本語

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1753
KeywordsTranscription / RNA polymerase / tRNA
SampleRNA polymerase III
SourceSaccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Map dataRNA-Polymerase III in its free form
Methodsingle particle reconstruction, at 21 Å resolution
AuthorsVannini A / Ringel R / Kusser AG / Berninghausen O / Kassavetis GA / Cramer P
CitationCell, 2010, 143, 59-70

Cell, 2010, 143, 59-70 Yorodumi Papers
Molecular basis of RNA polymerase III transcription repression by Maf1.
Alessandro Vannini / Rieke Ringel / Anselm G Kusser / Otto Berninghausen / George A Kassavetis / Patrick Cramer

DateDeposition: Jun 30, 2010 / Header (metadata) release: Jul 23, 2010 / Map release: Oct 8, 2010 / Last update: Dec 11, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0035
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1753.map.gz (map file in CCP4 format, 2849 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
3.31 Å/pix.
= 297.9 Å
90 pix
3.31 Å/pix.
= 297.9 Å
90 pix
3.31 Å/pix.
= 297.9 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.31 Å
Contour Level:0.0035 (by author), 0.0035 (movie #1):
Minimum - Maximum-0.00569051 - 0.253301
Average (Standard dev.)0.00280515 (0.0138798)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 297.9 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z297.900297.900297.900
start NX/NY/NZ-100-100-100
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0060.2530.003

Supplemental data

Sample components

Entire RNA polymerase III

EntireName: RNA polymerase III / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: Monomeric
MassTheoretical: 700 kDa / Experimental: 700 kDa / Measured by: Native Mass Spectrometry

Component #1: protein, RNA polymerase III

ProteinName: RNA polymerase III / a.k.a: RNA polymerase III / Oligomeric Details: Monomeric / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Strain: NZ-16
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Nucleus

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 20mM Hepes pH 7.8, 50 mM Ammonium Sulfate, 0.1 mM MgCl2, 0.01 mM ZnCl2, 5mM DTT
pH: 7.8
Support filmQuantifoil R3/3 2nm carbon pre-coated holey grids
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 184 K / Humidity: 95 % / Details: Vitrification instrument: Vitrobot, FEI

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 20480 / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 21 Å / Resolution method: FSC 0.5

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more