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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5138 | |||||||||
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Title | Lidless Mm-cpn in the closed state | |||||||||
![]() | This is a map of the lidless Mm-cpn in the nucleotide-induced closed state. | |||||||||
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![]() | Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone | |||||||||
Function / homology | ![]() chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Zhang J / Baker ML / Schroeder G / Douglas NR / Reissmann S / Jakana J / Dougherty M / Fu CJ / Levitt M / Ludtke SJ ...Zhang J / Baker ML / Schroeder G / Douglas NR / Reissmann S / Jakana J / Dougherty M / Fu CJ / Levitt M / Ludtke SJ / Frydman J / Chiu W | |||||||||
![]() | ![]() Title: Mechanism of folding chamber closure in a group II chaperonin. Authors: Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith ...Authors: Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu / ![]() Abstract: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings ...Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
Images | ![]() | 212.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j03M ![]() 5137C ![]() 5139C ![]() 5140C ![]() 3iyfC ![]() 3losC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | This is a map of the lidless Mm-cpn in the nucleotide-induced closed state. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Mm-cpn with 1mM ATP/AlFx
Entire | Name: Mm-cpn with 1mM ATP/AlFx |
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Components |
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-Supramolecule #1000: Mm-cpn with 1mM ATP/AlFx
Supramolecule | Name: Mm-cpn with 1mM ATP/AlFx / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 1 |
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Molecular weight | Experimental: 960 KDa / Theoretical: 960 KDa |
-Macromolecule #1: Lidless Methanococcus maripaludis Chaperonin
Macromolecule | Name: Lidless Methanococcus maripaludis Chaperonin / type: protein_or_peptide / ID: 1 / Name.synonym: Lidless Mm-cpn / Number of copies: 16 / Oligomeric state: 16-mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 960 KDa / Theoretical: 960 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 1 blot 3 seconds |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: in column omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 112000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: side-entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
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Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN |