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- EMDB-0036: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6... -

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Basic information

Entry
Database: EMDB / ID: EMD-0036
TitleStructure of activated transcription complex Pol II-DSIF-PAF-SPT6, upstream DNA selected particles (Map G)
Map dataGlobal refinement of upstream DNA selected EC* particles (Map G).
Sample
  • Complex: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
    • Complex: RNA Polymerase II
    • Complex: associated proteins
    • Complex: Nucleic acidsNucleic acid
Biological speciesSus scrofa (pig) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
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 /
Abstract: Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here ...Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.
History
DepositionMay 26, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseSep 5, 2018-
UpdateSep 12, 2018-
Current statusSep 12, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0062
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0062
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0036.png

Downloads & links

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Map

FileDownload / File: emd_0036.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal refinement of upstream DNA selected EC* particles (Map G).
Voxel sizeX=Y=Z: 1.049 Å
Density
Contour LevelBy AUTHOR: 0.0062 / Movie #1: 0.0062
Minimum - Maximum-0.019865137 - 0.059740696
Average (Standard dev.)0.0001798398 (±0.0020949878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.64 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0200.0600.000

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Supplemental data

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Mask #1

Fileemd_0036_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map of global refinement of upstream DNA...

Fileemd_0036_additional.map
AnnotationPostprocessed map of global refinement of upstream DNA selected EC* particles with an applied B factor of -94.30(Map G).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of global refinement for upstream...

Fileemd_0036_half_map_1.map
AnnotationHalf map 2 of global refinement for upstream DNA selected particles (Map G).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of global refinement for upstream...

Fileemd_0036_half_map_2.map
AnnotationHalf map 1 of global refinement for upstream DNA selected particles (Map G).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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*)
Components
  • Complex: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
    • Complex: RNA Polymerase II
    • Complex: associated proteins
    • Complex: Nucleic acidsNucleic acid

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

SupramoleculeName: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21, #23
Molecular weightTheoretical: 1.257 MDa

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Supramolecule #2: RNA Polymerase II

SupramoleculeName: RNA Polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9, #11, #10, #12
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: associated proteins

SupramoleculeName: associated proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13, #16, #18, #23, #19-#22
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: Nucleic acids

SupramoleculeName: Nucleic acids / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14-#15, #17
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 10s wait prior to blotting, blotting 8.5s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 313552
FSC plot (resolution estimation)

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