9R90 | pdb_00009r90

Cryo-EM structure of human ATP citrate lyase in complex with inhibitor EVT0185-CoA

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HXH

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.6681
f_angle_d	0.5596
f_chiral_restr	0.0414
f_plane_restr	0.0043
f_bond_d	0.0025

Sample
Human ATP citrate lyase (homotetramer)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Leica EM GP2

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	280072
Reported Resolution (Å)	3.25
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (6HXH)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value	138.8
Fitting Procedure
Details	Following 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the atomic models for the CSS and CSH modules (extracted from pdb 6xhx) were fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model. Cryo-EM map regions representing ligands in the ATP-grasp fold domain of the CCS module and in the CoA-binding domain were of the CSH module modelled as Mg.ADP and the adenosine 3'-phosphate 5'-diphosphate moiety of bound EVT0185-CoA, respectively. Restraints for EVT0185-CoA were generated via de Grade Web Server (https://grade.globalphasing.org).

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	61.8

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
Minimum Defocus (nm)	1200
Maximum Defocus (nm)	1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	JEOL CRYOSPECPORTER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v3.1.0
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	v3.1.0
MODEL FITTING	UCSF Chimera	1.17
MODEL REFINEMENT	PHENIX	1.20.1
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.1.0
FINAL EULER ASSIGNMENT	cryoSPARC	v3.1.0
CLASSIFICATION	cryoSPARC	v3.1.0
RECONSTRUCTION	cryoSPARC	v3.1.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		210900	Initial high-resolution 2D classes were obtained via the Blob Picker job in cryoSPARC, followed by template-based picking and neural network-based particle picking via TOPAZ as implemented in cryoSPARC. Ensuing 2D classification, 2D class selection and removal of potential duplicate particles within a distance of 150 Angstrom resulted in a particle set of 210,900 particles. Particles were extracted with a box size of 480 pixels with 2x binning.