8U8U

Cryo-EM Structure of Cognate Substrate ATP Bound in the Entry Site (ES) of Human Mitochondrial Transcription Elongation Complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OLA

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.436
f_angle_d	0.602
f_chiral_restr	0.04
f_plane_restr	0.005
f_bond_d	0.003

Sample
Cognate Substrate Bound in the Entry Site (ES) of Human Mitochondrial Transcription Elongation Complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	368317
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Non-uniform Refinement (CryoSPARC) which is an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps durin ...	Non-uniform Refinement (CryoSPARC) which is an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5OLA)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation Coefficient
Overall B Value	45
Fitting Procedure
Details	Initial Fitting was done in Chimera and flexible/refined fitting done with Coot Phenix Real-Space Refinement.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminary grid screening performed manually using TFS Glacios.

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5015:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4798227	Automated particle picking (Blob picker, CryoSPARC) with manual inspection (Inspect Particle Picks).

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.