Mammalian AP3 complex on tubular membranes (AP3 centered)
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Mammalian AP-3 complex assembled on tubular membranes
Specimen Preparation
Sample Aggregation State
HELICAL ARRAY
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
42469
Reported Resolution (Å)
7.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Alphafold 3 (AF3), was used to generate 5 models of mammalian AP3 in complex with two copies of ARF1 in the GTP bound conformation. As the structure f ...
Alphafold 3 (AF3), was used to generate 5 models of mammalian AP3 in complex with two copies of ARF1 in the GTP bound conformation. As the structure from STA was in a much more extended conformation than AF3 models or previous structures, direct rigid body docking of the complete AF3 model into the STA density was not possible. To create the C1 model the predicted complex was separated into three submodels, each of which was independently fitted into the map as a rigid body.
Submodel 1 consisted of sigma3 (1-193), delta (1-387), delta-ARF1 (1-181). Submodel 2 consisted of mu3 (1-418), beta3 (1-472), beta3-ARF1. Submodel 3 consisted of beta3 (473-636) and delta (388-638) formed submodel 3. Rigid body fitting was performed using ChimeraX. This positioned truncated regions of submodels 1 and 2 in close proximity to their adjoining regions in submodel3, thus the split beta3 and delta chains were rejoined into single chains before real-space refinement in COOT to correct bond angles, distances and torsions. Using the previously resolved ARF1 dimer (PDBID: 9C5A), ARF1 was first superimposed with the existing ARF1 on beta3 and delta before rigid docking into the EM density. Flexible regions not accounted for sufficiently by modellable density were removed, these regions are listed as follows; beta3 (1-42), beta3 (259-292), delta (1-17), sigma3 (154-193) and ARF1 (1-13). Side chains and rotamers were not modelled and were therefore removed in ChimeraX.
