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Yorodumi- PDB-6xhj: Cryo-EM structure of octadecameric TF55 (beta-only) complex from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xhj | |||||||||
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Title | Cryo-EM structure of octadecameric TF55 (beta-only) complex from S. solfataricus bound to ATP | |||||||||
Components | Thermosome subunit beta | |||||||||
Keywords | CHAPERONE / Chaperonin / Complex | |||||||||
Function / homology | Function and homology information ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Saccharolobus solfataricus (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
Authors | Zeng, Y.C. / Sobti, M. / Stewart, A.G. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2021 Title: Structural analysis of the Sulfolobus solfataricus TF55β chaperonin by cryo-electron microscopy. Authors: Yi Cheng Zeng / Meghna Sobti / Alastair G Stewart / Abstract: Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. ...Chaperonins are biomolecular complexes that assist in protein folding. Thermophilic factor 55 (TF55) is a group II chaperonin found in the archaeal genus Sulfolobus that has α, β and γ subunits. Using cryo-electron microscopy, structures of the β-only complex of S. solfataricus TF55 (TF55β) were determined to 3.6-4.2 Å resolution. The structures of the TF55β complexes formed in the presence of ADP or ATP highlighted an open state in which nucleotide exchange can occur before progressing in the refolding cycle. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6xhj.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhj.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhj ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhj | HTTPS FTP |
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-Related structure data
Related structure data | 22187MC 6xhiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: C1 (asymmetric)) |
-Components
#1: Protein | Mass: 60035.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / References: UniProt: Q9V2T8 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ATP-bound Octadecameric TF55 beta-subunit chaperonin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 1.08 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: 3.5 uL drop with 5 s blotting |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Average exposure time: 61 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1641 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 213286 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D9 (2x9 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53777 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4XCD Pdb chain-ID: A / Accession code: 4XCD / Source name: PDB / Type: experimental model |