[English] 日本語
Yorodumi- EMDB-0809: Cryo-electron tomography of Candidatus Prometheoarchaeum syntroph... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0809 | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-electron tomography of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 | ||||||||||||||||||||||||||||||||||||
Map data | Cryo-Electron tomography of MK-D1 | ||||||||||||||||||||||||||||||||||||
Sample |
| ||||||||||||||||||||||||||||||||||||
Biological species | anaerobic archaeon MK-D1 (archaea) | ||||||||||||||||||||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||||||||||||||||||||
Authors | Imachi 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
| ||||||||||||||||||||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0809.map.gz | 585.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0809-v30.xml emd-0809.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_0809.png | 195.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0809 | HTTPS FTP |
-Validation report
Summary document | emd_0809_validation.pdf.gz | 79.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0809_full_validation.pdf.gz | 78.3 KB | Display | |
Data in XML | emd_0809_validation.xml.gz | 498 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0809 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0809 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_0809.map.gz / Format: CCP4 / Size: 920.1 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-Electron tomography of MK-D1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Candidatus Prometheoarchaeum syntrophicum strain MK-D1
Entire | Name: Candidatus Prometheoarchaeum syntrophicum strain MK-D1 |
---|---|
Components |
|
-Supramolecule #1: Candidatus Prometheoarchaeum syntrophicum strain MK-D1
Supramolecule | Name: Candidatus Prometheoarchaeum syntrophicum strain MK-D1 type: cell / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: anaerobic archaeon MK-D1 (archaea) / Strain: MK-D1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Sugar embedding | Material: amorphous ice |
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Sigma-Aldrich / Diameter: 15 nm |
-Electron microscopy
Microscope | JEOL 2200FS |
---|---|
Temperature | Min: 76.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 FIELD / Cs: 4.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 15000 |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.15) / Number images used: 63 |
---|