Sequence-assignment validation in protein crystal structure models with checkMySequence.

Area of Science:

• Structural Biology
• Crystallography
• Biophysics

Background:

• Sequence register shifts are subtle errors in macromolecular models.
• These errors can compromise the interpretation of experimental data and affect subsequent model building.
• Previous work demonstrated a method for detecting these shifts in cryo-electron microscopy (cryo-EM) models.

Purpose of the Study:

• To adapt and validate a method for detecting sequence register shifts in X-ray crystal structure models.
• To demonstrate the utility of this method using standard crystallographic electron density maps.
• To identify and report sequence register errors in deposited protein data bank (PDB) models.

Main Methods:

• Systematic reassignment of short model fragments to the target sequence.
• Utilizing standard, model-bias-corrected electron density maps (2mFo - D Fc).
• Application of the fragment reassignment method to crystal structure models.

Main Results:

• The fragment reassignment method successfully detects sequence register shifts in crystal structures.
• Five distinct sequence register errors were identified in models within the Protein Data Bank (PDB).
• The method provides a reliable way to assess sequence-model correspondence.

Conclusions:

• The developed approach is effective for identifying sequence register errors in X-ray crystal structures.
• This method enhances the quality control of macromolecular models.
• Accurate macromolecular models are crucial for reliable biological interpretation and downstream research.