8X7U

MCM in complex with dsDNA in presence of ATP.

Summary for 8X7U

• Entry DOI: 10.2210/pdb8x7u/pdb
• EMDB information: 38111
• Descriptor: mini-chromosome maintenance complex 3, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: helicase, replication, hydrolase
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 6
• Total formula weight: 462156.33

Authors

Ma, J.,Yi, G.,Ye, M.,MacGregor-Chatwin, C.,Sheng, Y.,Lu, Y.,Li, M.,Gilbert, R.J.C.,Zhang, P. (deposition date: 2023-11-25, release date: 2024-01-17, Last modification date: 2025-01-01)

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 (3.57 Å)