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Open data
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Basic information
Entry | Database: PDB / ID: 3izn | ||||||
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Title | Mm-cpn deltalid with ATP | ||||||
![]() | Chaperonin | ||||||
![]() | CHAPERONE / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||
![]() | Douglas, N.R. / 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 986 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5250MC ![]() 5244C ![]() 5245C ![]() 5246C ![]() 5247C ![]() 5248C ![]() 5249C ![]() 3izhC ![]() 3iziC ![]() 3izjC ![]() 3izkC ![]() 3izlC ![]() 3izmC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: D8 (2x8 fold dihedral)) |
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Components
#1: Protein | Mass: 52618.535 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mm-cpn wildtype with ATP / Type: COMPLEX / Details: Methanococcus maripaludis chaperonin, 16-mer |
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Molecular weight | Value: 0.9 MDa / Experimental value: NO |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan side entry / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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Symmetry | Point symmetry: D8 (2x8 fold dihedral) | ||||||||||||
3D reconstruction | Resolution: 6.4 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT | ||||||||||||
Atomic model building | Space: REAL | ||||||||||||
Refinement step | Cycle: LAST
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