[English] 日本語
Yorodumi
- EMDB-65632: Subtomogram average of MJ1 attachment organelle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65632
TitleSubtomogram average of MJ1 attachment organelle
Map data
Sample
  • Organelle or cellular component: Subtomogram average of MJ1 attachment organelle
KeywordsS-layer / STRUCTURAL PROTEIN
Biological speciesNanobdella aerobiophila (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 22.3 Å
AuthorsGoto-Ito S / Yamagata A / Lee Y / Ehara H / Ito T
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H05281 Japan
Japan Society for the Promotion of Science (JSPS)JP23K05674 Japan
Japan Society for the Promotion of Science (JSPS)JP22K19141 Japan
Japan Agency for Medical Research and Development (AMED)JP24gm1410001 Japan
CitationJournal: J Biochem / Year: 2025
Title: Structural analysis of a symbiotic system involving a Nanobdellati archaeon by cryo-electron tomography.
Authors: Sakurako Goto-Ito / Shingo Kato / Mari Takahashi / Ayako Sakamoto / Atsushi Yamagata / Yongchan Lee / Haruhiko Ehara / Mayuko Sato / Kiminori Toyooka / Moriya Ohkuma / Takuhiro Ito /
Abstract: Nanobdellati (formerly DPANN) archaea are considered as primitive archaeal organisms that often live in symbiosis with archaeal hosts. In this study, we investigated the symbiotic mechanism between a ...Nanobdellati (formerly DPANN) archaea are considered as primitive archaeal organisms that often live in symbiosis with archaeal hosts. In this study, we investigated the symbiotic mechanism between a Nanobdellati archaeon, Nanobdella aerobiophila strain MJ1, and its host archaeon Metallosphaera sedula strain MJ1HA, using cryo-electron tomography. In our tomographic observations, we identified a conical attachment organelle at the interface between MJ1 and MJ1HA during symbiosis. This structure consists of a concentric array of short cylindrical shells, consistent with a previous report. Subtomogram averaging, combined with AlphaFold 3 structural predictions, allowed us to identify a potential component of attachment organelles. Additionally, we inferred potential components of the S-layers in MJ1 and MJ1HA based on tomographic data and subtomogram averages. Based on these analyses, we hypothesize that a MJ1 S-layer component may undergo conformational changes to also serve as a component of attachment organelles, warranting further investigation.
History
DepositionJul 31, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65632.png

Downloads & links

-
Map

FileDownload / File: emd_65632.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.18 Å/pix.
x 56 pix.
= 290.08 Å		5.18 Å/pix.
x 56 pix.
= 290.08 Å		5.18 Å/pix.
x 56 pix.
= 290.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.73
Minimum - Maximum-6.505965 - 6.409936
Average (Standard dev.)0.23892048 (±1.0353816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions565656
Spacing565656
CellA=B=C: 290.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_65632_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65632_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Subtomogram average of MJ1 attachment organelle

EntireName: Subtomogram average of MJ1 attachment organelle
Components
  • Organelle or cellular component: Subtomogram average of MJ1 attachment organelle

-
Supramolecule #1: Subtomogram average of MJ1 attachment organelle

SupramoleculeName: Subtomogram average of MJ1 attachment organelle / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Nanobdella aerobiophila (archaea)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 2.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.37 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 484
ExtractionNumber tomograms: 6 / Number images used: 497 / Software - Name: RELION
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more