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Yorodumi- EMDB-29443: Subtomogram average of 3-beta-ring hoop structure of M. hungatei ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29443 | |||||||||||||||
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Title | Subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath | |||||||||||||||
Map data | subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath | |||||||||||||||
Sample |
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Keywords | M. hungatei / archaeal sheath / cell wall / protein translocation / sheath assembly / cryoET / subtomogram average / amyloid-like protein / cell growth / STRUCTURAL PROTEIN | |||||||||||||||
Biological species | Methanospirillum hungatei JF-1 (archaea) | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 21.8 Å | |||||||||||||||
Authors | Wang H / Zhang J / Zhou ZH | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Hierarchical organization and assembly of the archaeal cell sheath from an amyloid-like protein. Authors: Hui Wang / Jiayan Zhang / Daniel Toso / Shiqing Liao / Farzaneh Sedighian / Robert Gunsalus / Z Hong Zhou / Abstract: Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath ...Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked β-hoops, each of which is comprised of two to six 400 nm-diameter rings of β-strand arches (β-rings). With both similarities to and differences from amyloid cross-β fibril architecture, each β-ring contains two giant β-sheets contributed by ~ 450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into β-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent β-hoops into the immature sheath cylinder at the junction of two daughter cells. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29443.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-29443-v30.xml emd-29443.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_29443.png | 5.1 KB | ||
Filedesc metadata | emd-29443.cif.gz | 4 KB | ||
Others | emd_29443_half_map_1.map.gz emd_29443_half_map_2.map.gz | 3.3 MB 3.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29443 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29443 | HTTPS FTP |
-Validation report
Summary document | emd_29443_validation.pdf.gz | 939.3 KB | Display | EMDB validaton report |
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Full document | emd_29443_full_validation.pdf.gz | 938.9 KB | Display | |
Data in XML | emd_29443_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | emd_29443_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29443 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29443 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29443.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.268 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1 of the subtomogram average of...
File | emd_29443_half_map_1.map | ||||||||||||
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Annotation | half map 1 of the subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2 of the subtomogram average of...
File | emd_29443_half_map_2.map | ||||||||||||
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Annotation | half map 2 of the subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Methanospirillum hungatei
Entire | Name: Methanospirillum hungatei |
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Components |
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-Supramolecule #1: Methanospirillum hungatei
Supramolecule | Name: Methanospirillum hungatei / type: cell / ID: 1 / Parent: 0 / Details: the whole cell of Methanospirillum hungatei |
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Source (natural) | Organism: Methanospirillum hungatei JF-1 (archaea) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) Details: The FSC was performed on 3dfsc online server https://3dfsc.salk.edu/ Number subtomograms used: 2971 |
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Extraction | Number tomograms: 10 / Number images used: 3323 |
Final angle assignment | Type: ANGULAR RECONSTITUTION |