|Entry||Database: EMDB / ID: 3818|
|Title||Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC4|
|Sample||RNA polymerase II-DSIF elongation complex|
|Source||Bos taurus / mammal / ウシ / |
Homo sapiens / human
|Map data||Locally filtered map, B-factor 0|
|Method||single particle reconstruction, at 3.7 Å resolution|
|Authors||Bernecky C / Plitzko JM / Cramer P|
|Citation||Nat. Struct. Mol. Biol., 2017, 24, 809-815|
|Date||Deposition: Jul 18, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Sep 13, 2017 / Last update: Oct 18, 2017|
Downloads & links
|File||emd_3818.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.35 Å|
CCP4 map header:
|File||emd_3818_msk_1.map ( map file in CCP4 format, 67109 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Space group number||1|
-Entire RNA polymerase II-DSIF elongation complex
|Entire||Name: RNA polymerase II-DSIF elongation complex / Number of components: 4|
|Mass||Theoretical: 690 kDa|
-Component #1: protein, RNA polymerase II-DSIF elongation complex
|Protein||Name: RNA polymerase II-DSIF elongation complex / Recombinant expression: No|
|Mass||Theoretical: 690 kDa|
-Component #2: protein, RNA polymerase II
|Protein||Name: RNA polymerase II / Recombinant expression: No|
|Mass||Theoretical: 520 kDa|
|Source||Species: Bos taurus / mammal / ウシ /|
-Component #3: protein, DSIF
|Protein||Name: DSIF / Recombinant expression: No|
|Mass||Theoretical: 130 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli|
-Component #4: protein, DNA-RNA synthetic construct
|Sample solution||Specimen conc.: 0.25 mg/ml / Buffer solution: pH was adjusted at 25 degrees Celsius / pH: 7.25|
|Vitrification||Instrument: 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.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 33 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 2549|
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 76394|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF|
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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