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- EMDB-45366: M. hungatei S-layer hexamer (C6) -

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Basic information

Entry
Database: EMDB / ID: EMD-45366
TitleM. hungatei S-layer hexamer (C6)
Map datamain map
Sample
  • Cell: Methanospirillum hungatei strain JF1 cells
KeywordsS-layer / M. hungatei / cellular lattice / hexamer / cell wall / Ig-like domain / STRUCTURAL PROTEIN
Biological speciesMethanospirillum hungatei JF-1 (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 6.4 Å
AuthorsWang H / Zhang J / Liao S / Zhou ZH / Gunsalus RP
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)1515843 United States
National Science Foundation (NSF, United States)1911781 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)1338135 United States
National Science Foundation (NSF, United States)1548924 United States
CitationJournal: Sci Adv / Year: 2024
Title: Composition and in situ structure of the cell envelope and surface layer.
Authors: Hui Wang / Jiayan Zhang / Shiqing Liao / Anne M Henstra / Deborah Leon / Jonathan Erde / Joseph A Loo / Rachel R Ogorzalek Loo / Z Hong Zhou / Robert P Gunsalus /
Abstract: Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo-electron ...Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo-electron tomography, we visualized the S-layer lattice surrounding , a methanogenic archaeon. Though more compact than known structures, 's S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer's cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment. cell's end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.
History
DepositionJun 14, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45366.png

Downloads & links

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Map

FileDownload / File: emd_45366.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 288 pix.
= 470.592 Å		1.63 Å/pix.
x 288 pix.
= 470.592 Å		1.63 Å/pix.
x 288 pix.
= 470.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.634 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.01709492 - 0.049422365
Average (Standard dev.)0.000000000000065 (±0.0064334064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 470.59198 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45366_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_45366_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_45366_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Methanospirillum hungatei strain JF1 cells

EntireName: Methanospirillum hungatei strain JF1 cells
Components
  • Cell: Methanospirillum hungatei strain JF1 cells

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Supramolecule #1: Methanospirillum hungatei strain JF1 cells

SupramoleculeName: Methanospirillum hungatei strain JF1 cells / type: cell / ID: 1 / Parent: 0
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: 2.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 46550
ExtractionNumber tomograms: 36 / Number images used: 64093 / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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