5FZ5

Transcription initiation complex structures elucidate DNA opening (CC)


ELECTRON MICROSCOPY
Sample
YEAST POL II TRANSCRIPTION INITIATION COMPLEX (CLOSED DNA)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsLIQUID ETHANE
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles5690
Reported Resolution (Å)8.8
Resolution Method
Other DetailsTHE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON ...THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE DOMAINS TFA1 AND TFA2 WH, 3.TFIIE TFA2 WH1 AND TFIIF TFG2 WH) WERE INDIVIDUALLY FITTED INTO THE CLOSED COMPLEX EM DENSITY BY AN AUTOMATED CORRELATION SEARCH IN SITUS. TO MODEL CLOSED PROMOTER DNA, UPSTREAM DNA WAS EXTENDED WITH CANONICAL DUPLEX B-FORM DNA IN COOT AND RIGID-BODY FITTED IN UCSF CHIMERA TO REFLECT THE DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3383. (DEPOSITION ID: 14367).
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment2016-06-20
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)5000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification37000
Calibrated Magnification37037
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
EACH PARTICLE