|Entry||Database: EMDB / ID: 1194|
|Title||Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.|
|Map data||3D reconstruction of human TFIID in solution (cryo E.M.), group 1|
|Sample||human TFIIDTranscription factor II D:|
TFIIDTranscription factor II D
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 33 Å resolution|
|Authors||Grob P / Cruse MJ / Inouye C / Peris M / Penczek PA / Tjian R / Nogales E|
|Citation||Journal: Structure / Year: 2006|
Title: Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues.
Authors: Patricia Grob / Michael J Cruse / Carla Inouye / Marian Peris / Pawel A Penczek / Robert Tjian / Eva Nogales
|Date||Deposition: Feb 24, 2006 / Header (metadata) release: Feb 28, 2006 / Map release: Feb 28, 2007 / Last update: Aug 31, 2011|
|Structure viewer||EM map: |
Downloads & links
|File||emd_1194.map.gz (map file in CCP4 format, 2077 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 5.06 Å|
CCP4 map header:
-Entire human TFIID
|Entire||Name: human TFIID|
Details: The sample was prepared from a single preparation of TFIID, immunopurified from HeLa cell nuclear extrats (TAF130 antibody)
Number of components: 1
|Mass||Theoretical: 1000 kDa / Experimental: 1000 kDa / Measured by: chromatography, sequence|
-Component #1: protein, TFIID
|Protein||Name: TFIIDTranscription factor II D / Recombinant expression: Yes|
|Mass||Theoretical: 1000 kDa / Experimental: 1000 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: HeLa|
|Source (natural)||Organelle: Nucleus / Location in cell: Nucleus / Cell: HeLa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.025 mg/ml|
Buffer solution: 25mM HEPES, 0.1 mM EDTA, 12.5mM MgCl2, 200mM KCl, 0.03% NP 40
|Support film||400 mesh copper grid with holey carbon|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 95 %|
Details: Vitrification instrument: Vitrobot. rince once with sample buffer before blotting
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 50200 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 5000 nm|
|Specimen Holder||Holder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 90 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 90 / Scanner: OTHER / Sampling size: 12.7 microns / Bit depth: 14|
|Processing||Method: single particle reconstruction / Number of projections: 4569 / Details: additional continuous thin carbon layer / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Simultaneous iterative reconstruction technique / Software: Spider, IMAGIC / CTF correction: whole micrograph / Resolution: 33 Å / Resolution method: FSC 0.5 / Euler angles: SPIDER, theta 90 degrees, phi 359.9|
Details: group1 selected using 3D variance calculation and 2D classification in high variance mask
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