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- EMDB-0030: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6... -

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Basic information

Entry
Database: EMDB / ID: 0030
TitleStructure of activated transcription complex Pol II-DSIF-PAF-SPT6 (Map B, NGN/SPT4 selected particles)
Map dataGlobal refinement of NGN/SPT4 selected particles.
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 / 3.34 Å resolution
AuthorsVos SM / Farnung L / Boehning M / Linden A / Wigge C / Urlaub H / Cramer P
CitationJournal: Nature / Year: 2018
Title: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.
Authors: Seychelle M Vos / Lucas Farnung / Marc Boehning / Christoph Wigge / Andreas Linden / Henning Urlaub / Patrick Cramer
DateDeposition: May 26, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Sep 5, 2018 / Last update: Sep 12, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0030.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.05 Å/pix.
= 377.64 Å
360 pix
1.05 Å/pix.
= 377.64 Å
360 pix
1.05 Å/pix.
= 377.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.049 Å
Density
Contour Level:0.00576 (by author), 0.008 (movie #1):
Minimum - Maximum-0.018119918 - 0.051605143
Average (Standard dev.)0.00018398488 (0.0020904206)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.0.0.
Limit359.359.359.
Spacing360360360
CellA=B=C: 377.64 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0491.0491.049
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z377.640377.640377.640
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0180.0520.000

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Supplemental data

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Mask #1

Fileemd_0030_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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

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

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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: 1.257 MDa

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Component #2: protein, RNA Polymerase II

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

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Component #3: protein, associated proteins

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

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Component #4: protein, Nucleic acids

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: 10s wait prior to blotting, blotting 8.5s.

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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: 4 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 130000. X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 105854
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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