9R90 | pdb_00009r90

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


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HXH 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.6681
f_angle_d0.5596
f_chiral_restr0.0414
f_plane_restr0.0043
f_bond_d0.0025
Sample
Human ATP citrate lyase (homotetramer)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification DetailsLeica EM GP2
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles280072
Reported Resolution (Å)3.25
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFollowing 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the at ...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 TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6HXH)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value138.8
Fitting Procedure
DetailsFollowing 3D classification, local refinement resulted in a cryo-EM volume with a golden standard FSC0.143-resolution of 3.25 Angstrom in which the at ...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 TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)61.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 300
Minimum Defocus (nm)1200
Maximum Defocus (nm)1800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelJEOL CRYOSPECPORTER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv3.1.0
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARCv3.1.0
MODEL FITTINGUCSF Chimera1.17
MODEL REFINEMENTPHENIX1.20.1
INITIAL EULER ASSIGNMENTcryoSPARCv3.1.0
FINAL EULER ASSIGNMENTcryoSPARCv3.1.0
CLASSIFICATIONcryoSPARCv3.1.0
RECONSTRUCTIONcryoSPARCv3.1.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION210900Initial 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.