DARC site

DARC site aligns cryo-electron microscopy (cryo-EM) maps and atomic coordinates of ribosomal complexes into a common coordinate system to enable direct structural comparison and analysis.

Key Features:

• Alignment of Structures: Aligns ribosomal particles from cryo-EM maps and atomic coordinates into a unified reference frame for direct comparison of conformational states.
• Extensive Data Repository: Contains over 130 cryo-EM maps and more than 300 atomic models encompassing multiple ribosomal states and complexes with protein factors, RNAs, and small molecules.
• File Format Support: Includes cryo-EM maps in brix format and atomic models in PDB format.
• Visualization of Conformational Dynamics: Provides aligned coordinates to visualize subunit rotation and head-swiveling across structures.
• Comparison of Ligand Interactions: Enables direct comparison of bound ligands, including antibiotics and translation factors, to assess interaction differences.

Scientific Applications:

• Ribosome structure–function analysis: Facilitates comparison of structural variations to interpret functional consequences for protein synthesis.
• Analysis of conformational dynamics during translation: Supports study of subunit rotation and head-swiveling associated with different translational states.
• Investigation of antibiotic mechanisms and therapeutic targeting: Enables comparative analysis of antibiotic and translation factor binding to inform mechanisms of action and therapeutic development.

Methodology:

Computational alignment of cryo-EM maps (brix) and atomic models (PDB) from EMDB and PDB into a unified coordinate system.