|Entry||Database: EMDB / ID: 8816|
|Title||TFIIH reconstruction from particles sorted for density near the XPD ARCH domain using signal-subtracted classification.|
|Sample||transcription factor IIH (TFIIH)|
|Source||Homo sapiens / human / Wikipedia|
|Map data||Human TFIIH reconstruction obtained from particle images sorted for density near the XPD ARCH domain using signal-subtracted classification|
|Method||single particle reconstruction, at 5.4 Å resolution|
|Authors||Greber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E|
|Citation||Nature, 2017, 549, 414-417|
|Date||Deposition: Jul 10, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Oct 4, 2017 / Last update: Feb 14, 2018|
Downloads & links
|File||emd_8816.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.32 Å|
CCP4 map header:
-Entire transcription factor IIH (TFIIH)
|Entire||Name: transcription factor IIH (TFIIH) / Number of components: 1|
|Mass||Theoretical: 490 kDa|
-Component #1: protein, transcription factor IIH (TFIIH)
|Protein||Name: transcription factor IIH (TFIIH) / Recombinant expression: No|
|Mass||Theoretical: 490 kDa|
|Source||Species: Homo sapiens / human / Wikipedia / Strain: HeLa|
|Source (natural)||Organelle: Nucleus / Location in cell: Nucleus|
|Sample solution||Specimen conc.: 0.0049 mg/ml / pH: 7.8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278.15 K / Humidity: 100 % / Details: 3-4 minute incubation, 2 second blot|
-Electron microscopy imaging
|Imaging||Microscope: FEI TITAN|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 37879 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4500 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 8300 / Sampling size: 5 microns|
Details: 8300 micrographs collected in four session with identical acquisition settings. Sessions lasted 4, 2, 4, and 4 days and yielded 1200, 1700, 2800, and 2600 micrographs.
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 35900|
Details: Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION|
CTF correction: Correction within RELION based on values determined in CTFFIND4.
Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: RELION 3D auto-refinement (gold standard). The final 3D classification used signal-subtracted particle images. The final reconstruction used the corresponding un-subtracted particle images.
Euler angles: Maximum-likelihood 3D refinement within RELION.
-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
-Jul 12, 2017. Major update of PDB
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