[English] 日本語
Yorodumi
- EMDB-13720: Cryo electron tomogram of purified AlgoCIS Cgo1 deficient mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13720
TitleCryo electron tomogram of purified AlgoCIS Cgo1 deficient mutant
Map data
Sample
  • Complex: The purified extracellular contractile injection system (AlgoCIS) Cgo1 deficient mutant
Biological speciesAlgoriphagus machipongonensis (bacteria)
Methodelectron tomography / cryo EM
AuthorsXu J / Ericson C / Feldmueller M / Lien YW / Eisenstein F / Pilhofer M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)679209 Switzerland
Swiss National Science Foundation31003A_179255 Switzerland
CitationJournal: Nat Microbiol / Year: 2022
Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis.
Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer /
Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
DepositionOct 11, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

-
Structure visualization

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

emd_13720.png

Downloads & links

-
Map

FileDownload / File: emd_13720.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 11 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)40.966137 (±18.628868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0175
Dimensions928960150
Spacing960928150
CellA: 10560.0 Å / B: 10208.0 Å / C: 1650.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z111111
M x/y/z960928150
origin x/y/z0.0000.0000.000
length x/y/z10560.00010208.0001650.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS1075
NC/NR/NS960928150
D min/max/mean-128.000127.00040.966

-
Supplemental data

-
Sample components

-
Entire : The purified extracellular contractile injection system (AlgoCIS)...

EntireName: The purified extracellular contractile injection system (AlgoCIS) Cgo1 deficient mutant
Components
  • Complex: The purified extracellular contractile injection system (AlgoCIS) Cgo1 deficient mutant

-
Supramolecule #1: The purified extracellular contractile injection system (AlgoCIS)...

SupramoleculeName: The purified extracellular contractile injection system (AlgoCIS) Cgo1 deficient mutant
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Algoriphagus machipongonensis (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: cytodiagnostics / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.1 e/Å2
Details: 2.1 electrons for each tilt, while total ~130 electron for one tilt series (61 tilts).
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

+
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://pdbjlvh1.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