Molecular basis of ZPD homopolymerization: cryo-EM structure of a native vertebrate egg coat filament
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Sample
Native chicken ZPD homopolymeric filament
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
Cryogen Name
NITROGEN
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
498339
Reported Resolution (Å)
4.6
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
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Model building was initiated using a local installation of AlphaFold 3 to predict a minimal filament fragment comprising one full-length subunit (chai ...
Model building was initiated using a local installation of AlphaFold 3 to predict a minimal filament fragment comprising one full-length subunit (chain A) and two partial subunits (chains B and C). The top-ranked prediction was rigid-body fitted into an initial 8.6 A-resolution map (postprocessed with EMReady2) using UCSF Chimera, followed by flexible fitting with Namdinator. Non-resolved terminal regions were trimmed, and well-defined N-glycan densities were manually built in Coot. The model was refined by real-space refinement in Phenix using NCS constraints and increased non-bonded interaction weights, followed by ADP refinement against the unsharpened map. This model served as a starting point for extension with an additional EGF and ZP-N domain from a fourth subunit (chain D). The extended model was docked into the present 4.6 A-resolution map, manually adjusted, and subjected to flexible fitting using the cryo-EM minimizer from cg2all; subsequently, it was refined using Refmac Servalcat task of CCP-EM Doppio, applying global NCS restraints, ProSMART-derived self-restraints, and increased non-bonded interaction weights. Following additional rounds of manual model rebuilding in Coot and real-space refinement in PHENIX (as described above), with positional refinement performed against a LocScale2-postprocessed map and ADP refinement against the unsharpened map, the model was validated using MolProbity and PHENIX.
Note that the EGF domain of chain A (and, to a lesser extent, portions of its ZP-N domain near the postprocessed map boundary and the distal regions of the EGF domains in chains C and D) are weakly defined in the density, consistent with their elevated B-factors. These regions were retained in the model to preserve biological completeness, with their conformations constrained by NCS during refinement.
