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- EMDB-0852: Cryo-electron tomography of Candidatus Prometheoarchaeum syntroph... -

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Entry
Database: EMDB / ID: EMD-0852
TitleCryo-electron tomography of Candidatus Prometheoarchaeum syntrophicum strain MK-D1
Map datatomogram of MK-D1
Sample
  • Cell: Candidatus Prometheoarchaeum syntrophicum strain MK-D1
Biological speciesanaerobic archaeon MK-D1 (archaea)
Methodelectron tomography / cryo EM
AuthorsImachi H / Nobu MK / Nakahara N / Morono Y / Ogawara M / Takaki Y / Takano Y / Uematsu K / Ikuta T / Ito M ...Imachi H / Nobu MK / Nakahara N / Morono Y / Ogawara M / Takaki Y / Takano Y / Uematsu K / Ikuta T / Ito M / Matsui Y / Miyazaki M / Murata K / Saito Y / Sakai S / Song C / Tasumi E / Yamanaka Y / Yamaguchi T / Kamagata Y / Tamaki H / Takai K
Funding support Japan, 11 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP16H06280 Japan
Japan Society for the Promotion of Science16J10845 Japan
Japan Society for the Promotion of Science18687006 Japan
Japan Society for the Promotion of Science24687011 Japan
Japan Society for the Promotion of Science21687006 Japan
Japan Society for the Promotion of Science19H01005 Japan
Japan Society for the Promotion of Science15H02419 Japan
Japan Society for the Promotion of Science26710012 Japan
Japan Society for the Promotion of Science18H03367 Japan
Japan Society for the Promotion of Science18H05295 Japan
Japan Society for the Promotion of Science18H02426 Japan
CitationJournal: Nature / Year: 2020
Title: Isolation of an archaeon at the prokaryote-eukaryote interface.
Authors: Hiroyuki Imachi / Masaru K Nobu / Nozomi Nakahara / Yuki Morono / Miyuki Ogawara / Yoshihiro Takaki / Yoshinori Takano / Katsuyuki Uematsu / Tetsuro Ikuta / Motoo Ito / Yohei Matsui / ...Authors: Hiroyuki Imachi / Masaru K Nobu / Nozomi Nakahara / Yuki Morono / Miyuki Ogawara / Yoshihiro Takaki / Yoshinori Takano / Katsuyuki Uematsu / Tetsuro Ikuta / Motoo Ito / Yohei Matsui / Masayuki Miyazaki / Kazuyoshi Murata / Yumi Saito / Sanae Sakai / Chihong Song / Eiji Tasumi / Yuko Yamanaka / Takashi Yamaguchi / Yoichi Kamagata / Hideyuki Tamaki / Ken Takai /
Abstract: The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic features that ...The origin of eukaryotes remains unclear. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E) model.
History
DepositionNov 3, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseDec 25, 2019-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_0852.png

Downloads & links

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Map

FileDownload / File: emd_0852.map.gz / Format: CCP4 / Size: 336.5 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotationtomogram of MK-D1
Voxel sizeX=Y=Z: 22.9 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)-40.514 (±27.550056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin130-130250
Dimensions980720500
Spacing720980500
CellA: 16488.0 Å / B: 22442.0 Å / C: 11450.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z22.922.922.9
M x/y/z720980500
origin x/y/z0.0000.0000.000
length x/y/z16488.00022442.00011450.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-130130250
NC/NR/NS720980500
D min/max/mean-128.000127.000-40.514

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Supplemental data

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Sample components

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Entire : Candidatus Prometheoarchaeum syntrophicum strain MK-D1

EntireName: Candidatus Prometheoarchaeum syntrophicum strain MK-D1
Components
  • Cell: Candidatus Prometheoarchaeum syntrophicum strain MK-D1

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Supramolecule #1: Candidatus Prometheoarchaeum syntrophicum strain MK-D1

SupramoleculeName: Candidatus Prometheoarchaeum syntrophicum strain MK-D1
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: anaerobic archaeon MK-D1 (archaea) / Strain: MK-D1

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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
Sugar embeddingMaterial: amorphous ice
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma-Aldrich / Diameter: 15 nm

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated defocus max: 4.9672 µm / Calibrated defocus min: 1.5783 µm / Calibrated magnification: 16717 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 15000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 76.0 K / Max: 77.0 K
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Frames/image: 3-25 / Number grids imaged: 1 / Number real images: 63 / Average exposure time: 1.0 sec. / Average electron dose: 1.5 e/Å2

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Image processing

Final reconstructionSoftware - Name: IMOD (ver. 4.7.15) / Number images used: 61

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