6O6C

RNA polymerase II elongation complex arrested at a CPD lesion

Summary for 6O6C

• Entry DOI: 10.2210/pdb6o6c/pdb
• EMDB information: 0633
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC4, RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3'), ... (15 entities in total)
• Functional Keywords: rna polymerase, cpd, elongation complex, streptavidin grids, transcription, transferase-dna-rna complex, transferase/dna/rna
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 13
• Total formula weight: 486531.04

Authors

Lahiri, I.,Leshziner, A.E. (deposition date: 2019-03-05, release date: 2019-06-26, Last modification date: 2024-03-20)

Primary citation

Lahiri, I.,Xu, J.,Han, B.G.,Oh, J.,Wang, D.,DiMaio, F.,Leschziner, A.E.
3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids.
J.Struct.Biol., 207:270-278, 2019

PubMed Abstract: Despite significant advances in all aspects of single particle cryo-electron microscopy (cryo-EM), specimen preparation still remains a challenge. During sample preparation, macromolecules interact with the air-water interface, which often leads to detrimental effects such as denaturation or adoption of preferred orientations, ultimately hindering structure determination. Randomly biotinylating the protein of interest (for example, at its primary amines) and then tethering it to a cryo-EM grid coated with two-dimensional crystals of streptavidin (acting as an affinity surface) can prevent the protein from interacting with the air-water interface. Recently, this approach was successfully used to solve a high-resolution structure of a test sample, a bacterial ribosome. However, whether this method can be used for samples where interaction with the air-water interface has been shown to be problematic remains to be determined. Here we report a 3.1 Å structure of an RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion (Pol II EC(CPD)) solved using streptavidin grids. Our previous attempt to solve this structure using conventional sample preparation methods resulted in a poor quality cryo-EM map due to Pol II EC(CPD)'s adopting a strong preferred orientation. Imaging the same sample on streptavidin grids improved the angular distribution of its view, resulting in a high-resolution structure. This work shows that streptavidin affinity grids can be used to address known challenges posed by the interaction with the air-water interface.

PubMed: 31200019
DOI: 10.1016/j.jsb.2019.06.004

Experimental method

ELECTRON MICROSCOPY (3.1 Å)