[English] 日本語
Yorodumi
- EMDB-27110: Intracellular Coxiella 48hpi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27110
TitleIntracellular Coxiella 48hpi
Map data
Sample
  • Cell: COS-7 cell infected with Coxiella 48hpi
Biological speciesCoxiella burnetii (bacteria)
Methodelectron tomography / cryo EM
AuthorsPark D / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI152421-02 United States
CitationJournal: Infect Immun / Year: 2022
Title: Developmental Transitions Coordinate Assembly of the Coxiella burnetii Dot/Icm Type IV Secretion System.
Authors: Donghyun Park / Samuel Steiner / Meng Shao / Craig R Roy / Jun Liu /
Abstract: Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique biphasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV), ...Coxiella burnetii is an obligate intracellular bacterial pathogen that has evolved a unique biphasic developmental cycle. The infectious form of C. burnetii is the dormant small cell variant (SCV), which transitions to a metabolically active large cell variant (LCV) that replicates inside the lysosome-derived host vacuole. A Dot/Icm type IV secretion system (T4SS), which can deliver over 100 effector proteins to host cells, is essential for the biogenesis of the vacuole and intracellular replication. How the distinct C. burnetii life cycle impacts the assembly and function of the Dot/Icm T4SS has remained unknown. Here, we combine advanced cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) imaging to visualize all developmental transitions and the assembly of the Dot/Icm T4SS . Importantly, assembled Dot/Icm machines were not present in the infectious SCV. The appearance of the assembled Dot/Icm machine correlated with the transition of the SCV to the LCV intracellularly. Furthermore, temporal characterization of C. burnetii morphological changes revealed regions of the inner membrane that invaginate to form tightly packed stacks during the LCV-to-SCV transition at late stages of infection, which may enable the SCV-to-LCV transition that occurs upon infection of a new host cell. Overall, these data establish how C. burnetii developmental transitions control critical bacterial processes to promote intracellular replication and transmission.
History
DepositionMay 26, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27110.png

Downloads & links

-
Map

FileDownload / File: emd_27110.map.gz / Format: CCP4 / Size: 1012.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.22 Å/pix.
x 128 pix.
= 2332.16 Å		18.22 Å/pix.
x 1440 pix.
= 26236.799 Å		18.22 Å/pix.
x 1440 pix.
= 26236.799 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: 18.22 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-26.185759 - 13.19662
Average (Standard dev.)-4.4414086e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-110
Dimensions14401440128
Spacing14401440128
CellA: 26236.799 Å / B: 26236.799 Å / C: 2332.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : COS-7 cell infected with Coxiella 48hpi

EntireName: COS-7 cell infected with Coxiella 48hpi
Components
  • Cell: COS-7 cell infected with Coxiella 48hpi

-
Supramolecule #1: COS-7 cell infected with Coxiella 48hpi

SupramoleculeName: COS-7 cell infected with Coxiella 48hpi / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Coxiella burnetii (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 kV / Focused ion beam - Current: 0.05 nA / Focused ion beam - Duration: 3600 sec. / Focused ion beam - Temperature: 103 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 33

+
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