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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5244 | |||||||||
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Title | Mm-cpn D386A with ATP | |||||||||
![]() | This is the density map of the Mm-cpn D386A mutant with ATP bound. | |||||||||
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![]() | Mm-cpn / maripaludis / chaperonin | |||||||||
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: 11.0 Å | |||||||||
![]() | Douglas NR / Reissmann S / Zhang J / Chen B / Jakana J / Kumar R / Chiu W / Frydman J | |||||||||
![]() | ![]() Title: Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Authors: Nicholai R Douglas / Stefanie Reissmann / Junjie Zhang / Bo Chen / Joanita Jakana / Ramya Kumar / Wah Chiu / Judith Frydman / ![]() Abstract: Group II chaperonins are ATP-dependent ring-shaped complexes that bind nonnative polypeptides and facilitate protein folding in archaea and eukaryotes. A built-in lid encapsulates substrate proteins ...Group II chaperonins are ATP-dependent ring-shaped complexes that bind nonnative polypeptides and facilitate protein folding in archaea and eukaryotes. A built-in lid encapsulates substrate proteins within the central chaperonin chamber. Here, we describe the fate of the substrate during the nucleotide cycle of group II chaperonins. The chaperonin substrate-binding sites are exposed, and the lid is open in both the ATP-free and ATP-bound prehydrolysis states. ATP hydrolysis has a dual function in the folding cycle, triggering both lid closure and substrate release into the central chamber. Notably, substrate release can occur in the absence of a lid, and lid closure can occur without substrate release. However, productive folding requires both events, so that the polypeptide is released into the confined space of the closed chamber where it folds. Our results show that ATP hydrolysis coordinates the structural and functional determinants that trigger productive folding. | |||||||||
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 | ![]() | 23 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.2 KB 8.2 KB | Display Display | ![]() |
Images | ![]() | 142.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 328.5 KB | Display | ![]() |
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Full document | ![]() | 328 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3izhMC ![]() 5245C ![]() 5246C ![]() 5247C ![]() 5248C ![]() 5249C ![]() 5250C ![]() 3iziC ![]() 3izjC ![]() 3izkC ![]() 3izlC ![]() 3izmC ![]() 3iznC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the density map of the Mm-cpn D386A mutant with ATP bound. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 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 D386A with ATP
Entire | Name: Mm-cpn D386A with ATP |
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Components |
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-Supramolecule #1000: Mm-cpn D386A with ATP
Supramolecule | Name: Mm-cpn D386A with ATP / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 1 |
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Molecular weight | Experimental: 900 KDa / Theoretical: 900 KDa |
-Macromolecule #1: chaperonin
Macromolecule | Name: chaperonin / type: protein_or_peptide / ID: 1 / Name.synonym: Mm-cpn / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 900 KDa / Theoretical: 900 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 |
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Electron microscopy
Microscope | JEOL 2010F |
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Image recording | Category: FILM / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Scanner: OTHER |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Gatan side entry / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN |
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