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Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Specimen Preparation
Sample Aggregation State
CELL
Vitrification Instrument
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SUBTOMOGRAM AVERAGING
Number of Particles
1001
Reported Resolution (Å)
17
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
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body f ...
Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body fitted into the open conformation of the map, and the AlphaFold3 multimer prediction of subcomplex SecYEG-DF was aligned to and replaced the old AlphaFold2 models of these proteins.
The SecYEG-DF subcomplex as well as the remaining proteins were each rigid body fitted as single rigid bodies using ChimeraX fit-to-map.