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Basic information

Database: EMDB / ID: EMD-1754
Map data
SampleRNA polymerase III-DNA-RNA complex:
RNA polymerase III / nucleic-acidNucleic acid
KeywordsTranscription / RNA polymerase / tRNA
Biological speciesSaccharomyces cerevisiae (baker's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 19 Å
AuthorsVannini A / Ringel R / Kusser AG / Berninghausen O / Kassavetis GA / Cramer P
CitationJournal: Cell / Year: 2010
Title: Molecular basis of RNA polymerase III transcription repression by Maf1.
Authors: Alessandro Vannini / Rieke Ringel / Anselm G Kusser / Otto Berninghausen / George A Kassavetis / Patrick Cramer /
Abstract: RNA polymerase III (Pol III) transcribes short RNAs required for cell growth. Under stress conditions, the conserved protein Maf1 rapidly represses Pol III transcription. We report the crystal ...RNA polymerase III (Pol III) transcribes short RNAs required for cell growth. Under stress conditions, the conserved protein Maf1 rapidly represses Pol III transcription. We report the crystal structure of Maf1 and cryo-electron microscopic structures of Pol III, an active Pol III-DNA-RNA complex, and a repressive Pol III-Maf1 complex. Binding of DNA and RNA causes ordering of the Pol III-specific subcomplex C82/34/31 that is required for transcription initiation. Maf1 binds the Pol III clamp and rearranges C82/34/31 at the rim of the active center cleft. This impairs recruitment of Pol III to a complex of promoter DNA with the initiation factors Brf1 and TBP and thus prevents closed complex formation. Maf1 does however not impair binding of a DNA-RNA scaffold and RNA synthesis. These results explain how Maf1 specifically represses transcription initiation from Pol III promoters and indicate that Maf1 also prevents reinitiation by binding Pol III during transcription elongation.
DepositionJun 30, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseOct 8, 2010-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0019
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_1754.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.31 Å
Contour LevelBy AUTHOR: 0.0019 / Movie #1: 0.0019
Minimum - Maximum-0.00533559 - 0.216791
Average (Standard dev.)0.00274789 (±0.0133266)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 297.9 Å
α=β=γ: 90 °

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-0.0050.2170.003

Supplemental data

Sample components

Entire RNA polymerase III-DNA-RNA complex

EntireName: RNA polymerase III-DNA-RNA complex / Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: Dimeric
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: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: NZ-16
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)
Source (natural)Location in cell: nucleus

Component #2: nucleic-acid, DNA-RNA elongation scaffold

nucleic acidName: DNA-RNA elongation scaffold / a.k.a: DNA-RNA elongation scaffold / Class: DNA/RNA / Structure: OTHER / Synthetic: Yes
SourceSpecies: synthetic construct (others)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
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: 11965 / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 19 Å / Resolution method: FSC 0.5

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