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- EMDB-10489: Structure of complete, activated transcription complex Pol II-DSI... -

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Database: EMDB / ID: EMD-10489
TitleStructure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 (Map 10)
Map data
SampleComplete EC*
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsVos SM / Farnung L / Cramer P
Funding support Germany, 4 items
OrganizationGrant numberCountry
European Research Council693023 Germany
German Research FoundationSFB860 Germany
German Research FoundationSFB860 Germany
Volkswagen Foundation Germany
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
Authors: Seychelle M Vos / Lucas Farnung / Andreas Linden / Henning Urlaub / Patrick Cramer /
Abstract: Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation ...Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation.
DepositionNov 12, 2019-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_10489.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 377.64 Å
1.05 Å/pix.
x 360 pix.
= 377.64 Å
1.05 Å/pix.
x 360 pix.
= 377.64 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.049 Å
Contour LevelBy AUTHOR: 0.0145 / Movie #1: 0.017
Minimum - Maximum-0.01736568 - 0.06390071
Average (Standard dev.)0.00039535467 (±0.003159411)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0170.0640.000

Supplemental data

Half map: Half map 1

AnnotationHalf map 1
Projections & Slices


Slices (1/2)
Density Histograms

Half map: Half map 2

AnnotationHalf map 2
Projections & Slices


Slices (1/2)
Density Histograms

Sample components

Entire Complete EC*

EntireName: Complete EC* / Number of components: 1

Component #1: protein, Complete EC*

ProteinName: Complete EC* / Recombinant expression: No
MassTheoretical: 1.34 MDa
SourceSpecies: Homo sapiens (human)

Experimental details

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: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s..

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: 40 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 130000 X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: GIF Bioquantum
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 13679

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35713
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6GMH, 4L1U, 6AFO
Overall bvalue: 115

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