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- EMDB-42579: Subtomogram average of the the Metallosphaera javensis AS-7 prime... -

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Basic information

Entry
Database: EMDB / ID: EMD-42579
TitleSubtomogram average of the the Metallosphaera javensis AS-7 primed nanotube
Map dataSubtomogram average of the the Metallosphaera javensis AS-7 primed nanotube.
Sample
  • Complex: Metallosphaera javensis AS-7 nanotube
KeywordsDPANN / Intercellular communication / Protein nanotube / STRUCTURAL PROTEIN
Biological speciesMetallosphaera javensis (ex Sakai et al. 2022) (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 27.3 Å
AuthorsGhosal D / Johnson MD / Shepherd D
Funding support Australia, France, Japan, 5 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1196924 Australia
Human Frontier Science Program (HFSP)RGEC33/2023 France
Japan Society for the Promotion of Science (JSPS)21K15153 Japan
Australian Research Council (ARC)FT200100270 Australia
Australian Research Council (ARC)DP210100362 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Cell-to-cell interactions revealed by cryo-tomography of a DPANN co-culture system.
Authors: Matthew D Johnson / Doulin C Shepherd / Hiroyuki D Sakai / Manasi Mudaliyar / Arun Prasad Pandurangan / Francesca L Short / Paul D Veith / Nichollas E Scott / Norio Kurosawa / Debnath Ghosal /
Abstract: DPANN is a widespread and diverse group of archaea characterized by their small size, reduced genome, limited metabolic pathways, and symbiotic existence. Known DPANN species are predominantly ...DPANN is a widespread and diverse group of archaea characterized by their small size, reduced genome, limited metabolic pathways, and symbiotic existence. Known DPANN species are predominantly obligate ectosymbionts that depend on their host for proliferation. The structural and molecular details of host recognition, host-DPANN intercellular communication, and host adaptation in response to DPANN attachment remain unknown. Here, we use electron cryotomography (cryo-ET) to show that the Microcaldus variisymbioticus ARM-1 may interact with its host, Metallosphaera javensis AS-7 through intercellular proteinaceous nanotubes. Combining cryo-ET and sub-tomogram averaging, we show the in situ architectures of host and DPANN S-layers and the structures of the nanotubes in their primed and extended states. In addition, comparative proteomics and genomic analyses identified host proteomic changes in response to DPANN attachment. These results provide insights into the structural basis of host-DPANN communication and deepen our understanding of the host ectosymbiotic relationships.
History
DepositionNov 1, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42579.png

Downloads & links

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Map

FileDownload / File: emd_42579.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the the Metallosphaera javensis AS-7 primed nanotube.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.39 Å/pix.
x 168 pix.
= 569.52 Å		3.39 Å/pix.
x 168 pix.
= 569.52 Å		3.39 Å/pix.
x 168 pix.
= 569.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-11.251307000000001 - 9.4977255
Average (Standard dev.)0.054135133 (±1.0000252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 569.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42579_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Metallosphaera javensis AS-7 nanotube

EntireName: Metallosphaera javensis AS-7 nanotube
Components
  • Complex: Metallosphaera javensis AS-7 nanotube

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Supramolecule #1: Metallosphaera javensis AS-7 nanotube

SupramoleculeName: Metallosphaera javensis AS-7 nanotube / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Metallosphaera javensis (ex Sakai et al. 2022) (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: 3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsCultures of Metallosphaera javensis AS-7 were routinely cultivated at 55 degrees Celsius using modified Brocks basal salt medium supplemented with 1 g/L yeast extract (MBSY medium). The pH of the medium was adjusted to 3.0 by the addition of 50 % (v/v) sulfate.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 27.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.99) / Number subtomograms used: 797
ExtractionNumber tomograms: 28 / Number images used: 797 / Method: Manual picking / Software - Name: EMAN2 (ver. 2.99)
Final 3D classificationSoftware - Name: EMAN2 (ver. 2.99)
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 2.99)
FSC plot (resolution estimation)

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