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Structure paper

TitleOpen architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 10304, Year 2024
Publish dateNov 27, 2024
AuthorsJianbing Ma / Gangshun Yi / Mingda Ye / Craig MacGregor-Chatwin / Yuewen Sheng / Ying Lu / Ming Li / Qingrong Li / Dong Wang / Robert J C Gilbert / Peijun Zhang /
PubMed AbstractThe cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging ...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.
External linksNat Commun / PubMed:39604363 / PubMed Central
MethodsEM (single particle)
Resolution2.98 - 6.94 Å
Structure data

38109

8x7t

EMDB-38109, PDB-8x7t:
MCM in the Apo state.
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-38110: Structure of MCM_apo before local refinement
Method: EM (single particle) / Resolution: 3.26 Å

38111

8x7u

EMDB-38111, PDB-8x7u:
MCM in complex with dsDNA in presence of ATP.
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-38112: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-38113: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-38114: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-38115: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-38116: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-38117: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 3.31 Å

EMDB-38118: local refinement of MCM_apo
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-38119: MCM_ATP_dsDNA before local refinement
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-38120: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.41 Å

EMDB-38121: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.38 Å

EMDB-38122: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.55 Å

EMDB-38123: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-38124: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-38125: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-38126: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 6.64 Å

EMDB-38127: local refinement of MCM_ATP_dsDNA
Method: EM (single particle) / Resolution: 6.94 Å

61286

9ja0

EMDB-61286, PDB-9ja0:
The capsid protein of HIV 1
Method: EM (single particle) / Resolution: 3.14 Å

61287

9ja1

EMDB-61287, PDB-9ja1:
The RNA polymerase II elongation complex from Saccharomyces cerevisiae
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-ZN:
Unknown entry

Source
  • thermococcus kodakarensis (archaea)
  • human immunodeficiency virus 1
  • saccharomyces cerevisiae (brewer's yeast)
  • synthetic construct (others)
KeywordsHYDROLASE / Helicase / Replication / VIRAL PROTEIN / HIV 1 / Capsid protein / Di-Hexamer / BIOSYNTHETIC PROTEIN / RNA polymerase / elongation complex

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