9JA1

The RNA polymerase II elongation complex from Saccharomyces cerevisiae

Summary for 9JA1

• Entry DOI: 10.2210/pdb9ja1/pdb
• EMDB information: 61287
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB4, DNA-directed RNA polymerase II subunit RPB7, ... (17 entities in total)
• Functional Keywords: rna polymerase, elongation complex, biosynthetic protein
• Biological source: Saccharomyces cerevisiae (brewer's yeast); More
• Total number of polymer chains: 14
• Total formula weight: 549167.21

Authors

Yi, G.,Ma, J.,Zhang, P. (deposition date: 2024-08-23, release date: 2024-09-04, Last modification date: 2024-12-11)

Primary citation

Ma, J.,Yi, G.,Ye, M.,MacGregor-Chatwin, C.,Sheng, Y.,Lu, Y.,Li, M.,Li, Q.,Wang, D.,Gilbert, R.J.C.,Zhang, P.
Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.
Nat Commun, 15:10304-10304, 2024

PubMed Abstract: The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging proteins and complexes, especially those with low abundance or with preferential orientation, remains a major hurdle. We developed an affinity-grid method employing monodispersed single particle streptavidin on a lipid monolayer to enhance particle absorption on the grid surface and alleviate sample exposure to the air-water interface. Using this approach, we successfully enriched the Thermococcus kodakarensis mini-chromosome maintenance complex 3 (MCM3) on cryoEM grids through biotinylation and resolved its structure. We further utilized this affinity method to tether the biotin-tagged dsDNA to selectively enrich a stable MCM3-ATP-dsDNA complex for cryoEM structure determination. Intriguingly, both MCM3 apo and dsDNA bound structures exhibit left-handed open spiral conformations, distinct from other reported MCM structures. The large open gate is sufficient to accommodate a dsDNA which could potentially be melted. The value of mspSA affinity method was further demonstrated by mitigating the issue of preferential angular distribution of HIV-1 capsid protein hexamer and RNA polymerase II elongation complex from Saccharomyces cerevisiae.

PubMed: 39604363
DOI: 10.1038/s41467-024-53745-w

Experimental method

ELECTRON MICROSCOPY (2.98 Å)