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TitleCryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 4754, Year 2021
Publish dateAug 6, 2021
AuthorsYanyan Zhao / Michael F Schmid / Judith Frydman / Wah Chiu /
PubMed AbstractChaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism ...Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.
External linksNat Commun / PubMed:34362932 / PubMed Central
MethodsEM (single particle)
Resolution3.9 - 6.4 Å
Structure data

EMDB-24324, PDB-7r9e:
Methanococcus maripaludis chaperonin, open conformation 1
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-24325, PDB-7r9h:
Methanococcus maripaludis chaperonin, open conformation 2
Method: EM (single particle) / Resolution: 6.3 Å

EMDB-24326, PDB-7r9i:
Methanococcus maripaludis chaperonin, open conformation 2
Method: EM (single particle) / Resolution: 6.4 Å

EMDB-24327, PDB-7r9j:
Methanococcus maripaludis chaperonin, open conformation 4
Method: EM (single particle) / Resolution: 6.3 Å

EMDB-24328, PDB-7r9k:
Methanococcus maripaludis chaperonin, closed conformation 4
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-24329, PDB-7r9m:
Methanococcus maripaludis chaperonin, closed conformation 2
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-24330, PDB-7r9o:
Methanococcus maripaludis chaperonin, closed conformation 1
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-24331, PDB-7r9u:
Methanococcus maripaludis chaperonin, closed conformation 3
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-24363, PDB-7rak:
Methanococcus maripaludis chaperonin complex in open conformation
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

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

Source
  • methanococcus maripaludis (archaea)
KeywordsCHAPERONE / Open conformation / Closed conformation / Complex / chaperonin.

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