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- EMDB-3816: Structure of an RNA polymerase II-DSIF transcription elongation c... -

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Basic information

Entry
Database: EMDB / ID: 3816
TitleStructure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC2
SampleRNA polymerase II-DSIF elongation complex
SourceBos taurus / mammal / ウシ /
Homo sapiens / human
Synthetic construct
Map dataNone
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsBernecky C / Plitzko JM / Cramer P
CitationNat. Struct. Mol. Biol., 2017, 24, 809-815

Nat. Struct. Mol. Biol., 2017, 24, 809-815 Yorodumi Papers
Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Carrie Bernecky / Jürgen M Plitzko / Patrick Cramer

DateDeposition: Jul 18, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Sep 13, 2017 / Last update: Oct 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_3816.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.23098513 - 0.36672285
Average (Standard dev.)-1.1585955E-5 (0.010266359)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2310.367-0.000

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Supplemental data

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Mask #1

Fileemd_3816_msk_1.map ( map file in CCP4 format, 67109 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsNone
Space group number1

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Mask #1~

Fileemd_3816_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 elongation complex

EntireName: RNA polymerase II-DSIF elongation complex / Number of components: 4
MassTheoretical: 690 kDa

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Component #1: protein, RNA polymerase II-DSIF elongation complex

ProteinName: RNA polymerase II-DSIF elongation complex / Recombinant expression: No
MassTheoretical: 690 kDa

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Component #2: protein, RNA polymerase II

ProteinName: RNA polymerase II / Recombinant expression: No
MassTheoretical: 520 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #3: protein, DSIF

ProteinName: DSIF / Recombinant expression: No
MassTheoretical: 130 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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Component #4: protein, DNA-RNA synthetic construct

ProteinName: DNA-RNA synthetic construct / Recombinant expression: No
MassTheoretical: 40 kDa
SourceSpecies: Synthetic construct
Source (engineered)Expression System: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.25 mg/ml / Buffer solution: pH was adjusted at 25 degrees Celsius / pH: 7.25
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.

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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: 33 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000 X (nominal), 37037 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 3600 nm / Energy filter: GIF Quantum / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2549
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 139075
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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