Cryo-EM Analysis in CASP16

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Experimentalists are encouraged to submit cryo-electron microscopy (cryo-EM) data and atomic models for assessment in CASP.
• CASP16 saw 38 cryo-EM datasets submitted, representing most targets, often with a single atomic structure provided.

Purpose of the Study:

• To investigate the relationship between local resolution in cryo-EM reconstructions and the flexibility of predicted protein structures.
• To evaluate the accuracy of CASP predictions by comparing them with experimental cryo-EM data and local resolution information.

Main Methods:

• Analysis of 38 cryo-EM datasets from CASP16.
• Correlation analysis between local resolution in cryo-EM maps and root-mean-square fluctuations (RMSF) of residues in CASP predictions.
• Assessment of sidechain details using a variant of SMOC with local fragment alignment.

Main Results:

• Local resolution in cryo-EM reconstructions shows a good correlation with the root-mean-square fluctuations (RMSF) of residues in accurate CASP predictions.
• The correlation between local resolution and pLDDT was less clear, particularly with mobile domains.
• Assessment of sidechains revealed areas for improvement in high-quality predictions and identified modeling discrepancies in some targets.

Conclusions:

• Local resolution in cryo-EM data serves as a valuable indicator of structural flexibility in predicted models.
• Experimental cryo-EM data is crucial for model-free assessment, enabling unique analyses like comparison to local resolution.
• Discrepancies between predictions and experimental density highlight areas where modeling needs refinement.