[English] 日本語
Yorodumi
- EMDB-55870: Roseiflexus cells from microbial mat with contractile injection s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55870
TitleRoseiflexus cells from microbial mat with contractile injection systems.
Map data
Sample
  • Cell: Contracted contractile injection system in lysed Roseiflexus cell from microbial mat
Keywordscontractile injection system microbial mat Roseiflexus / VIRUS LIKE PARTICLE
Biological speciesRoseiflexus (bacteria)
Methodelectron tomography / cryo EM
AuthorsGaisin AV
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG 101000232European Union
CitationJournal: ISME J / Year: 2026
Title: Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.
Authors: Vasil A Gaisin / Corina Hadjicharalambous / Izabela Mujakić / Cristian Villena-Alemany / Jiangning Li / Michal Koblížek / Martin Pilhofer /
Abstract: Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs ...Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.
History
DepositionNov 27, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55870.png

Downloads & links

-
Map

FileDownload / File: emd_55870.map.gz / Format: CCP4 / Size: 843.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.04 Å/pix.
x 300 pix.
= 5412. Å		18.04 Å/pix.
x 1440 pix.
= 25977.602 Å		18.04 Å/pix.
x 1024 pix.
= 18472.961 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: 18.04 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-409.0 - 353.0
Average (Standard dev.)4.010861 (±22.156140000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-150
Dimensions14401024300
Spacing10241440300
CellA: 18472.96 Å / B: 25977.602 Å / C: 5412.0005 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Contracted contractile injection system in lysed Roseiflexus cell...

EntireName: Contracted contractile injection system in lysed Roseiflexus cell from microbial mat
Components
  • Cell: Contracted contractile injection system in lysed Roseiflexus cell from microbial mat

-
Supramolecule #1: Contracted contractile injection system in lysed Roseiflexus cell...

SupramoleculeName: Contracted contractile injection system in lysed Roseiflexus cell from microbial mat
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Roseiflexus (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 360 / Focused ion beam - Temperature: 123 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Zeiss Crossbeam. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61
CTF correctionType: NONE

+
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