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- EMDB-0041: Structure of paused transcription complex Pol II-DSIF-NELF, (Map 4) -

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Basic information

Database: EMDB / ID: 0041
TitleStructure of paused transcription complex Pol II-DSIF-NELF, (Map 4)
Map dataGlobally refined upstream DNA, NGN, KOW1 selected particles (Map 4).
SampleRNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*):
RNA Polymerase II / associated proteins / Nucleic acidsNucleic acid
SourceSus scrofa (pig) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsVos SM / Farnung L / Urlaub H / Cramer P
CitationJournal: Nature / Year: 2018
Title: Structure of paused transcription complex Pol II-DSIF-NELF.
Authors: Seychelle M Vos / Lucas Farnung / Henning Urlaub / Patrick Cramer
DateDeposition: May 27, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Sep 5, 2018 / Last update: Sep 12, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_0041.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.23 Å/pix.
= 314.291 Å
256 pix
1.23 Å/pix.
= 314.291 Å
256 pix
1.23 Å/pix.
= 314.291 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2277 Å
Contour Level:0.0055 (by author), 0.0055 (movie #1):
Minimum - Maximum-0.008213097 - 0.023484569
Average (Standard dev.)0.000117879674 (0.0014477392)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 314.2912 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.227699218751.227699218751.22769921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.291314.291314.291
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0080.0230.000

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

Entire RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)

EntireName: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
Number of components: 4

Component #1: protein, RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)

ProteinName: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
Recombinant expression: No
MassTheoretical: 927.1 kDa

Component #2: protein, RNA Polymerase II

ProteinName: RNA Polymerase II / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

Component #3: protein, associated proteins

ProteinName: associated proteins / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

Component #4: protein, Nucleic acids

ProteinName: Nucleic acidsNucleic acid / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 46 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 165000. X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 11740

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 29197
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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