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Yorodumi- EMDB-6291: 16 Angstrom cryo-EM reconstruction of the alpha, beta, gamma TF55... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6291 | |||||||||
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Title | 16 Angstrom cryo-EM reconstruction of the alpha, beta, gamma TF55 chaperonin | |||||||||
Map data | Cryo-EM reconstruction of the Sulfolobus solfataricus TF55 alpha/beta/gamma chaperonin | |||||||||
Sample |
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Keywords | TF55 chaperonin / protein folding / Sulfolobus solfataricus / cryo-EM | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Chaston JJ / Stewart AG / Smits C / Aragao D / Struwe W / Benesch J / Xwong A / Ling M / Ashsan B / Sandin S ...Chaston JJ / Stewart AG / Smits C / Aragao D / Struwe W / Benesch J / Xwong A / Ling M / Ashsan B / Sandin S / Rhodes D / Molugu SK / Bernal RA / Stock D | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins. Authors: Jessica J Chaston / Callum Smits / David Aragão / Andrew S W Wong / Bilal Ahsan / Sara Sandin / Sudheer K Molugu / Sanjay K Molugu / Ricardo A Bernal / Daniela Stock / Alastair G Stewart / Abstract: Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the ...Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6291.map.gz | 3.3 MB | EMDB map data format | |
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Header (meta data) | emd-6291-v30.xml emd-6291.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6291_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_6291.jpg | 824.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6291 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6291 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6291.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of the Sulfolobus solfataricus TF55 alpha/beta/gamma chaperonin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.174 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cryo-EM reconstruction of the TF55 chaperonin containing the alph...
Entire | Name: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits |
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Components |
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-Supramolecule #1000: Cryo-EM reconstruction of the TF55 chaperonin containing the alph...
Supramolecule | Name: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits type: sample / ID: 1000 Oligomeric state: Octadecamer composed of 6 alpha, 6 beta, and 6 gamma subunits per complex Number unique components: 1 |
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Molecular weight | Theoretical: 1.08 MDa / Method: sequence |
-Macromolecule #1: TF55 chaperonin
Macromolecule | Name: TF55 chaperonin / type: protein_or_peptide / ID: 1 Details: The TF55 chaperonin is composed of three proteins (alpha, beta, and gamma) arranged in an alternating fashion to form a 9-subunit ring (3 of each protein) which then stacks back-to-back with ...Details: The TF55 chaperonin is composed of three proteins (alpha, beta, and gamma) arranged in an alternating fashion to form a 9-subunit ring (3 of each protein) which then stacks back-to-back with a second ring, forming an 18-subunit complex. Number of copies: 18 / Oligomeric state: octadecamer / Recombinant expression: Yes |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) / Strain: DSM1617 |
Molecular weight | Theoretical: 1 MDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pETDUET (Novagen) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris-Cl, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 50 mM NaCl |
Grid | Details: 400-mesh copper grid with holey carbon film support (Quantifoil R2/2) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 108 K / Instrument: HOMEMADE PLUNGER Method: 3 microliters of sample were blotted off the Quantifoil R2/2 grid for 3 seconds before plunging. |
-Electron microscopy
Microscope | JEOL 3200FS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 69000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000 |
Specialist optics | Energy filter - Name: JEOL in-column / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Sample stage | Specimen holder: 626 Gatan holder / Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 83 K / Max: 103 K / Average: 93 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification. |
Date | Jun 20, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 16534 / Average electron dose: 25 e/Å2 / Bits/pixel: 8 |