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- EMDB-29443: Subtomogram average of 3-beta-ring hoop structure of M. hungatei ... -

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Basic information

Entry
Database: EMDB / ID: EMD-29443
TitleSubtomogram average of 3-beta-ring hoop structure of M. hungatei sheath
Map datasubtomogram average of 3-beta-ring hoop structure of M. hungatei sheath
Sample
  • Cell: Methanospirillum hungatei
KeywordsM. hungatei / archaeal sheath / cell wall / protein translocation / sheath assembly / cryoET / subtomogram average / amyloid-like protein / cell growth / STRUCTURAL PROTEIN
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 21.8 Å
AuthorsWang H / Zhang J / Zhou ZH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1515843 United States
National Science Foundation (NSF, United States)1911781 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
Department of Energy (DOE, United States)DE-FC-02-02ER63421 United States
CitationJournal: 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
DepositionJan 12, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29443.png

Downloads & links

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Map

FileDownload / File: emd_29443.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of 3-beta-ring hoop structure of M. hungatei sheath
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.27 Å/pix.
x 120 pix.
= 392.16 Å		3.27 Å/pix.
x 120 pix.
= 392.16 Å		3.27 Å/pix.
x 120 pix.
= 392.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.023080273 - 0.030426336
Average (Standard dev.)-0.000000001091392 (±0.00595106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 392.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1 of the subtomogram average of...

Fileemd_29443_half_map_1.map
Annotationhalf map 1 of the subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of the subtomogram average of...

Fileemd_29443_half_map_2.map
Annotationhalf map 2 of the subtomogram average of 3-beta-ring hoop structure of M. hungatei sheath
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Methanospirillum hungatei

EntireName: Methanospirillum hungatei
Components
  • Cell: Methanospirillum hungatei

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Supramolecule #1: Methanospirillum hungatei

SupramoleculeName: Methanospirillum hungatei / type: cell / ID: 1 / Parent: 0 / Details: the whole cell of Methanospirillum hungatei
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Final reconstructionApplied 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
ExtractionNumber tomograms: 10 / Number images used: 3323
Final angle assignmentType: ANGULAR RECONSTITUTION

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