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Open data
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Basic information
Entry | Database: PDB / ID: 3j1b | ||||||
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Title | Cryo-EM structure of 8-fold symmetric rATcpn-alpha in apo state | ||||||
![]() | Chaperonin alpha subunit | ||||||
![]() | CHAPERONE / Group II chaperonin | ||||||
Function / homology | ![]() ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||
![]() | Zhang, K. / Wang, L. / Liu, Y.X. / Wang, X. / Gao, B. / Hu, Z.J. / Ji, G. / Chan, K.Y. / Schulten, K. / Dong, Z.Y. / Sun, F. | ||||||
![]() | ![]() Title: Flexible interwoven termini determine the thermal stability of thermosomes. Authors: Kai Zhang / Li Wang / Yanxin Liu / Kwok-Yan Chan / Xiaoyun Pang / Klaus Schulten / Zhiyang Dong / Fei Sun / ![]() Abstract: Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II ...Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II chaperonin assembly and thermal stability is yet to be elucidated. Here, we selected the group II chaperonins (cpn-α and cpn-β), also called thermosomes, from Acidianus tengchongensis and investigated their assembly and thermal stability. We found that the binding of ATP or its analogs contributed to the successful assembly of thermosomes and enhanced their thermal stabilities. Cpn-β is more thermally stable than cpn-α, while the thermal stability of the hetero thermosome cpn-αβ is intermediate. Cryo-electron microscopy reconstructions of cpn-α and cpn-β revealed the interwoven densities of their non-conserved flexible N/C-termini around the equatorial planes. The deletion or swapping of their termini and pH-dependent thermal stability assays revealed the key role of the termini electrostatic interactions in the assembly and thermal stability of the thermosomes. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | 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 | ![]() 5391MC ![]() 5392C ![]() 5395C ![]() 5396C ![]() 3j1cC ![]() 3j1eC ![]() 3j1fC ![]() 3j1d ![]() 3j1g ![]() 3j1h ![]() 3j1i ![]() 3j1j ![]() 3j1k ![]() 3j1l 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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Components
#1: Protein | Mass: 60269.285 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: 8-fold symmetric rATcpn-alpha in apo state / Type: COMPLEX Details: hexadecamer. This sample has about 90% 8-fold symmetric particles and 10% 9-fold symmetric particles Synonym: Thermosome |
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Buffer solution | Name: Tris-HCl / pH: 7.5 / Details: Tris-HCl |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: This sample was applied to a 400-mesh GiG grid with holes of 2 um diameter and 2 um spacing. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 100 % Details: Blot for 4 seconds before plunging into liquid nitrogen (FEI Vitrobot Mark IV). |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 23, 2010 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Calibrated magnification: 96000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Details: 4k x 4k |
Image scans | Num. digital images: 3424 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
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CTF correction | Details: The whole micrograph | ||||||||||||||||
Symmetry | Point symmetry: C8 (8 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 4.9 Å / Num. of particles: 55460 / Details: Spider, EMAN1.9 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: METHOD--symmetry-restrained MDFF REFINEMENT PROTOCOL--Rigid body and Molecular Dynamics Flexible Fitting | ||||||||||||||||
Atomic model building | PDB-ID: 3KO1 Accession code: 3KO1 / Source name: PDB / Type: experimental model | ||||||||||||||||
Refinement step | Cycle: LAST
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