cryo-EM structure of ribonucleotide reductase from Synechococcus phage S-CBP4 bound with TTP
ELECTRON MICROSCOPY
Sample
Ribonucleotide reductase from Synechoccus phage S-CBP4 bound with TTP
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
blot for 4 seconds before plunging
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
107885
Reported Resolution (Å)
3.46
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
74.37
Fitting Procedure
Details
The sequence for the ribonucleotide reductase from Synechococcus phage S-CBP4 was retrieved from UniProt with accession number M1PRZ0. The sequence wa ...
The sequence for the ribonucleotide reductase from Synechococcus phage S-CBP4 was retrieved from UniProt with accession number M1PRZ0. The sequence was used as input for AlphaFold2 prediction with the five default model parameters and a template date cutoff of 2020-05-14. As the five models were largely identical in the core region and differing only in the location of the C-terminal tail, the structure predicted with the first model parameter was used in the subsequent process. The predicted structure was first processed and docked into the unsharpened map in phenix. The 25 N-terminal residues and 45 C-terminal residues were then manually removed due to lack of cryo-EM density, and residues 26-426 were retained in the model. We observed unmodeled density at the specificity site, and based on solution composition, we modeled a TTP molecule. The TTP molecule with magnesium ion from the crystal structure of Bacillus subtilis RNR (pdb: 6mt9) was extracted and rigid body fit into the unmodeled density in Coot. The combined model was refined with the unsharpened and sharpened maps using phenix.real_space_refine, with a constraint applied on the magnesium ion coordinated by the triphosphate in TTP according to the original configuration. Residue and loop conformations in the resulting structure were manually adjusted in Coot to maximize fit to map and input for an additional round of real-space refinement in phenix with an additional restraint for the disulfide bond between C30 and C196. Due to poor density of the magnesium ion, it was removed when deposited into PDB.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
50
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS TALOS
Minimum Defocus (nm)
600
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
OTHER
Nominal Magnification
79000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
Data was collected on a Thermo Fisher Talos Arcica Cryo-TEM with a Gatan K3 camera and BioQuantum energy filter.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
3.3.1
IMAGE ACQUISITION
SerialEM
3.8
CTF CORRECTION
cryoSPARC
3.3.1
MODEL FITTING
PHENIX
1.20.1
INITIAL EULER ASSIGNMENT
cryoSPARC
3.3.1
FINAL EULER ASSIGNMENT
cryoSPARC
3.3.1
RECONSTRUCTION
cryoSPARC
3.3.1
MODEL REFINEMENT
PHENIX
1.20.1
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
581884
46 high quality micrographs were then selected, from which the blob picker routine was used to pick particles. The resulting 99k particles were extracted and subjected to 2D classification, and the top four unique 2D classes were selected and used as templates for template picking on the entire dataset. Due to the large variance in ice conditions in many of our micrographs, masks were manually defined for every micrograph, and particle picks outside the ideal ice region were excluded.