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- EMDB-5159: About 8.8 angstrom cryo-electron structure of the recombinant Aci... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5159 | |||||||||
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Title | About 8.8 angstrom cryo-electron structure of the recombinant Acidianus tengchongensis chaperonin beta-APO. | |||||||||
![]() | This is an cryoEM structure density map of chaperonin rATcpnB-APO. | |||||||||
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![]() | rATcpn-beta-APO / Group II chaperonin / Thermosome | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
![]() | Huo Y / Hu Z / Zhang K / Wang L / Zhai Y / Zhou Q / Lander G / Zhu J / He Y / Pang X ...Huo Y / Hu Z / Zhang K / Wang L / Zhai Y / Zhou Q / Lander G / Zhu J / He Y / Pang X / Xu W / Bartlam M / Dong Z / Sun F | |||||||||
![]() | ![]() Title: Crystal structure of group II chaperonin in the open state. Authors: Yanwu Huo / Zhongjun Hu / Kai Zhang / Li Wang / Yujia Zhai / Qiangjun Zhou / Gabe Lander / Jiang Zhu / Yongzhi He / Xiaoyun Pang / Wei Xu / Mark Bartlam / Zhiyang Dong / Fei Sun / ![]() Abstract: Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle ...Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to a lack of high-resolution structure in the open state. Here, we report the first complete crystal structure of thermosome (rATcpnβ) in the open state from Acidianus tengchongensis. There is a ∼30° rotation of the apical and lid domains compared with the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain, and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpnβ were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from the open to the closed state. Structural comparison as well as protease K digestion indicated only ATP binding without hydrolysis does not induce chamber closure of thermosome. | |||||||||
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 | ![]() | 20.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 301.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.3 KB | Display | ![]() |
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Full document | ![]() | 78.4 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an cryoEM structure density map of chaperonin rATcpnB-APO. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.55 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 : rAtcpn beta-APO
Entire | Name: rAtcpn beta-APO |
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Components |
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-Supramolecule #1000: rAtcpn beta-APO
Supramolecule | Name: rAtcpn beta-APO / type: sample / ID: 1000 / Oligomeric state: 18 homo subunits / Number unique components: 1 |
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Molecular weight | Theoretical: 1.08 MDa |
-Macromolecule #1: rATcpn-beta-APO
Macromolecule | Name: rATcpn-beta-APO / type: protein_or_peptide / ID: 1 / Name.synonym: chaperonin beta-APO / Number of copies: 18 / Oligomeric state: 18mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.08 MDa |
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
Concentration | 8 mg/mL |
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Buffer | pH: 8 |
Grid | Details: C-flat |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 81 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: Blot for 6 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 1.55 µm / Number real images: 273 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: OTHER / Software - Name: EMAN, SPIDER / Number images used: 40000 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: chimera,EM-IMO |
Details | PDBEntryID_givenInChain. Protocol: Rigid Body, flexible fitting |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |