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- EMDB-3443: Electron cryo-microscopy of the yeast RNA polymerase I - Rrn3 com... -

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Basic information

Entry
Database: EMDB / ID: 3443
TitleElectron cryo-microscopy of the yeast RNA polymerase I - Rrn3 complex at 7.5A resolution
Map datareconstruction of the RNA pol I - Rrn3 complex
Samplecomplex formed between YEAST RNA polymerase I and the initiation factor Rrn3:
DNA dependent RNA polymerase I / Rrn3
KeywordsRNA polymerase I initiation factor Rrn3 transcription initiation
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / 7.5 Å resolution
AuthorsPilsl M / Crucifix C / Papai G / Krupp F / Steinbauer R / Griesenbeck J / Milkereit P / Tschochner H / Schultz P
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the initiation-competent RNA polymerase I and its implication for transcription.
Authors: Michael Pilsl / Corinne Crucifix / Gabor Papai / Ferdinand Krupp / Robert Steinbauer / Joachim Griesenbeck / Philipp Milkereit / Herbert Tschochner / Patrick Schultz
DateDeposition: Jul 21, 2016 / Header (metadata) release: Sep 28, 2016 / Map release: Sep 28, 2016 / Last update: Oct 12, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3443.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.16 Å/pix.
= 276.48 Å
128 pix
2.16 Å/pix.
= 276.48 Å
128 pix
2.16 Å/pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density
Contour Level:0.121 (by author), 0.121 (movie #1):
Minimum - Maximum-0.17636499 - 0.38812745
Average (Standard dev.)0.00050278 (0.02722943)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 276.48 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.162.162.16
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1760.3880.001

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Supplemental data

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Sample components

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Entire complex formed between YEAST RNA polymerase I and the initiation ...

EntireName: complex formed between YEAST RNA polymerase I and the initiation factor Rrn3
Number of components: 2 / Oligomeric State: 1
MassTheoretical: 663 MDa

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Component #1: protein, DNA dependent RNA polymerase I

ProteinName: DNA dependent RNA polymerase I / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (natural)Location in cell: nucleolar

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Component #2: protein, Rrn3

ProteinName: Rrn3 / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 72.346 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (natural)Location in cell: nucleolar

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 0.01 mg/ml
Buffer solution: 20 mM Hepes, 100mM ammonium acetate and 2mM MgCl2
pH: 7.8
Support filmsample was adsorbed on a floated carbon foil which was deposited onto a quantifoil grid
Stainingunstained
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Method: blotting time (4 sec.) blotting force 5

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jun 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 59000 X (nominal), 129630 X (calibrated) / Astigmatism: Cs corrector / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 90 K ( 80 - 100 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 32438
3D reconstructionAlgorithm: relion / Software: relion / CTF correction: each particle / Details: final map was calculated from 2 averaged datasets / Resolution: 7.5 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: gEMfitter, Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 4C2M

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