Home EMD-2308 Mirrors RCSB (USA) EBI (UK)  Contact EMDataBank

Title: Structural visualization of key steps in human transcription initiation Authors: He Y, Fang J, Taatjes DJ, Nogales E Sample: TBP-TFIIA-TFIIB-DNA-Pol II-TFIIF-TFIIE-TFIIH (close) Method: Single particle reconstruction (14 angstroms resolution) Latest update: 2013-04-10   Summary  Experimental details   Visualization   Map information   Downloads Sample Sample name: TBP-TFIIA-TFIIB-DNA-Pol II-TFIIF-TFIIE-TFIIH (close) Theoretical molecular weight of the sample: 1.35 Components: ID Type Name Exp. MW (MDa) Oligomeric details Recombinant expression Synthetic Organism UniProt identifier GO identifier InterPro identifier Virus identifier Details 1 protein TATA-box-binding protein true Homo sapiens 2 protein General transcription factor IIA true Homo sapiens 3 protein General transcription factor IIB true Homo sapiens 4 protein General transcription factor IIF true Homo sapiens 5 protein General transcription factor IIE true Homo sapiens 6 protein General transcription factor IIH false Homo sapiens 7 protein DNA-directed RNA polymerase II false Homo sapiens 8 nucleic-acid Core promoter DNA true Homo sapiens Experiment Specimen state: Particle Specimen preparation: pH Specimen conc. Details Staining Specimen support details 7.9 0.06 mg/mL 10 mM HEPES, 5% glycerol, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.05% NP-40 Grids with adsorbed protein floated on 2% w/v uranyl formate for 1 minute. 200 mesh Cu grid Vitrification: Cryogen name Humidity Temp. Instr. Method Time resolved Details NONE % K NONE ms Imaging: Microscope Voltage Illumination mode Imaging mode Cs Defocus min. Defocus max. Nominal mag. Calibrated mag. Electron source Detector Detector distance Astigmatism FEI TECNAI F20 120 kV FLOOD BEAM BRIGHT FIELD 2.2 mm 500 nm 1200 nm 80000 80000 FIELD EMISSION GUN Gatan Ultrascan 4000 mm objective lens astigmatism was corrected at 250,000 times magnification. Specimen holder Holder model Tilt min. Tilt max. Energy filter Energy window Temp. Temp. min. Temp. max. Beam tilt Electron dose Other details Date Room temp single tilt SIDE ENTRY, EUCENTRIC ° ° eV K K K mrad 20 e/Å2 Data acquired using Leginon 15-APR-2012 Processing Protocol: Projection matching Software: EMAN2, SPARX CTF correction: whole micrograph Number of particles: 64712 Imposed symmetry: C1 Resolution by author: 14 Å Resolution method: FSC at 0.143 cut-off Processing details: Image processing was performed in the Appion processing environment. 3D reconstruction was performed using EMAN2 and SPARX libraries. Final map was filtered to local resolution using the blocres function in Bsoft package. Scanned images: Num. images Sampling size OD range Quant. bit number Other details Scanner 600 μm/pixel Fitting: PDB Protocol Target crit. Software B value Fitting space PDB chain Details