Over 10K nucleic-acid-containing structures in the PDB

When visiting the RCSB PDB website today, I am please to notice that the PDB now contains “10015 Nucleic Acid Containing Structures”. Based on “Macromolecule Type” in “Advanced Search” of the RCSB PDB website, I observed the following information:

  • The number of DNA-containing structures is 6,384 (reported in 2,997 papers), and the corresponding number for RNA-containing structures is 3,861 (associated with 2,012 publications).
  • There are 4,570 structures containing both DNA and protein (potentially forming DNA-protein complexes), and 2,478 RNA-protein complexes.
  • The smallest nucleic-acid-containg structures have only two nucleotides (e.g., 3rec), and largest ones are the ribosomes (and virus particles).
  • The earliest released DNA structure from the PDB is 1zna (on March 18, 1981), a Z-DNA tetramer. The earliest RNA structure released is 4tna (on April 12, 1978), a refined structure of the yeast phenylalanine transfer RNA.

This landmark achievement is made possible by the world-wide scientific community through decades of efforts solving DNA/RNA 3D structures via experimental approaches (mainly solution NMR, x-ray crystal, and cryo-EM). These over 10K nucleic acid structures present both challenges and opportunities for the field of structural bioinformatics, especially for intricate RNA molecules. DSSR is an integrated software tool for dissecting the spatial structure of RNA. It is my effort in addressing the challenging issues for the analysis/annotation and visualization of RNA structures.





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