9S34 | pdb_00009s34

Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther 
in silico modelAlphaFoldAF-Q9V122-F1 
Sample
20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3)
Sample Components
20S Proteasome from P. abyssi
Archaeal proteasome activator 1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles50092
Reported Resolution (Å)3.15
Resolution MethodFSC 0.143 CUT-OFF
Other Details50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.2 ...50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.23 Angstrom, which served as a base for the focused refinements used to make this composite map. Upon reconstruction with imposed C7 symmetry, the two proteasome Beta1-2 subunits of the 20S became merged together. We noticed that the same was happening when the 20S proteasome was reconstructed without an imposed symmetry, suggesting a random distribution of the two subunit types in the Beta rings. Due to the high degree of similarity between the two proteins (>70 percent sequence identity) and the small number of particles, we opted for not continuing with further 3D classification.
Refinement Type
Symmetry TypePOINT
Point SymmetryC7
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross correlation
Overall B Value
Fitting Procedure
DetailsModel building done in coot, refinement in Phenix. No models built for the merged Beta 1-2 chains of the 20S proteasome, due to the identical folding ...Model building done in coot, refinement in Phenix. No models built for the merged Beta 1-2 chains of the 20S proteasome, due to the identical folding of the two proteins and the very small (single side chains) differences between the two subunits, which prevented effective 3D classification with the small number of particles left. IMPORTANT: the outlier Y204 nonplanar bond was modelled as such based on a higher resolution X-ray model, to be deposited soon.
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS GLACIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.5
IMAGE ACQUISITIONSerialEM
MODEL FITTINGUCSF ChimeraX1.8
INITIAL EULER ASSIGNMENTcryoSPARC
FINAL EULER ASSIGNMENTcryoSPARC
RECONSTRUCTIONcryoSPARC4.5
MODEL REFINEMENTPHENIX1.21.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION534489