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- EMDB-69767: Nerearchaeum marumarumayae interaction with gram negative bacterium -

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Basic information

Entry
Database: EMDB / ID: EMD-69767
TitleNerearchaeum marumarumayae interaction with gram negative bacterium
Map data
Sample
  • Cell: Nerearchaeum marumarumayae interaction with gram negative bacterium
KeywordsArchaea / Asgard / UNKNOWN FUNCTION
Biological speciesPromethearchaeati (Asgard group)
Methodelectron tomography / cryo EM
AuthorsJohnson MD / Shepherd DC / Ghosal D
Funding support Australia, France, 3 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100769 Australia
Human Frontier Science Program (HFSP)RGEC33/2023 France
National Health and Medical Research Council (NHMRC, Australia)APP1196924 Australia
CitationJournal: Curr Biol / Year: 2026
Title: An Asgard archaeon from a modern analog of ancient microbial mats.
Authors: Stephanie-Jane Nobs / Matthew D Johnson / Timothy J Williams / Julia Meltzer / Xabier Vázquez-Campos / Fraser I MacLeod / Keiran Rowell / Miranda Pitt / Bindusmita Paul / Doulin C Shepherd ...Authors: Stephanie-Jane Nobs / Matthew D Johnson / Timothy J Williams / Julia Meltzer / Xabier Vázquez-Campos / Fraser I MacLeod / Keiran Rowell / Miranda Pitt / Bindusmita Paul / Doulin C Shepherd / Katharine A Michie / Iain G Duggin / Debnath Ghosal / Brendan P Burns /
Abstract: One of the most significant events in the evolution of life is the origin of the eukaryotic cell. Despite recent advances, the driving forces behind the emergence of complex eukaryotic attributes ...One of the most significant events in the evolution of life is the origin of the eukaryotic cell. Despite recent advances, the driving forces behind the emergence of complex eukaryotic attributes remain a gap in our knowledge. One model proposes that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea in ancient microbial mats. Here, we describe a highly enriched (89%) culture of a novel Asgard archaeon, Nerearchaeum marumarumayae, along with a bacterium Stromatodesulfovibrio nilemahensis from a modern microbial mat. The N. marumarumayae genome indicates that it has the capacity to produce H, acetate, formate, and sulfite, while S. nilemahensis synthesizes amino acids and vitamins that could be exchanged in a syntrophic partnership. Electron cryotomography revealed that N. marumarumayae cells produce chains of budded envelope vesicles attached to the coccoid cell body by extracellular fibers, as well as intracellular tube- and cage-like structures. Furthermore, the two species were observed directly interacting via intercellular tubular fibers assembled by the bacterium. These characteristics and interactions may reflect an early step in the symbiotic evolution of eukaryotic cells.
History
DepositionMar 17, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69767.png

Downloads & links

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Map

FileDownload / File: emd_69767.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.82 Å/pix.
x 300 pix.
= 3846. Å		12.82 Å/pix.
x 720 pix.
= 9230.399 Å		12.82 Å/pix.
x 512 pix.
= 6563.84 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 12.82 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-259.035829999999976 - 219.987580000000008
Average (Standard dev.)20.897000999999999 (±19.409469999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-150
Dimensions720512300
Spacing512720300
CellA: 6563.84 Å / B: 9230.399 Å / C: 3846.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nerearchaeum marumarumayae interaction with gram negative bacterium

EntireName: Nerearchaeum marumarumayae interaction with gram negative bacterium
Components
  • Cell: Nerearchaeum marumarumayae interaction with gram negative bacterium

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Supramolecule #1: Nerearchaeum marumarumayae interaction with gram negative bacterium

SupramoleculeName: Nerearchaeum marumarumayae interaction with gram negative bacterium
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Promethearchaeati (Asgard group)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV / Details: Manual back blot.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: sigma aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 53000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 53000
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 reconstructionSoftware - Name: IMOD (ver. 4.11) / Number images used: 35
CTF correctionType: NONE

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