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Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
experimental model
Other
in silico model
AlphaFold
AF-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 State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
50092
Reported Resolution (Å)
3.15
Resolution Method
FSC 0.143 CUT-OFF
Other Details
50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.2 ...
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 Type
POINT
Point Symmetry
C7
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Cross correlation
Overall B Value
Fitting Procedure
Details
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 ...
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.