[English] 日本語
Yorodumi
- EMDB-49122: In situ cryoET of an EPI vesicle in a Goslar infected chmA KD E. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49122
TitleIn situ cryoET of an EPI vesicle in a Goslar infected chmA KD E. coli cell 30 mpi
Map data
Sample
  • Cell: Goslar infected chmA KD E. coli cell 30 mpi
Keywordsvesicle / phage / genome / VIRUS
Biological speciesEscherichia coli (E. coli)
Methodelectron tomography / cryo EM / Resolution: 10.0 Å
AuthorsKlusch N / Villa E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Host Microbe / Year: 2025
Title: Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection.
Authors: Emily G Armbruster / Phoolwanti Rani / Jina Lee / Niklas Klusch / Joshua Hutchings / Lizbeth Y Hoffman / Hannah Buschkaemper / Eray Enustun / Benjamin A Adler / Koe Inlow / Arica R VanderWal ...Authors: Emily G Armbruster / Phoolwanti Rani / Jina Lee / Niklas Klusch / Joshua Hutchings / Lizbeth Y Hoffman / Hannah Buschkaemper / Eray Enustun / Benjamin A Adler / Koe Inlow / Arica R VanderWal / Madelynn Y Hoffman / Daksh Daksh / Ann Aindow / Amar Deep / Zaida K Rodriguez / Chase J Morgan / Majid Ghassemian / Thomas G Laughlin / Emeric Charles / Brady F Cress / David F Savage / Jennifer A Doudna / Kit Pogliano / Kevin D Corbett / Elizabeth Villa / Joe Pogliano /
Abstract: Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family ...Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic viruses. Bacteriophages of the Chimalliviridae family sequester their genomes within a phage-generated organelle, the phage nucleus, which is enclosed by a lattice of the viral protein ChmA. We show that inhibiting phage nucleus formation arrests infections at an early stage in which the injected phage genome is enclosed within a membrane-bound early phage infection (EPI) vesicle. Early phage genes are expressed from the EPI vesicle, demonstrating its functionality as a prokaryotic, transcriptionally active, membrane-bound organelle. We also show that the phage nucleus is essential, with genome replication beginning after the injected DNA is transferred from the EPI vesicle to the phage nucleus. Our results show that Chimalliviridae require two sophisticated subcellular compartments of distinct compositions and functions that facilitate successive stages of the viral life cycle.
History
DepositionFeb 7, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49122.png

Downloads & links

-
Map

FileDownload / File: emd_49122.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 518 pix.
= 5180. Å		10 Å/pix.
x 996 pix.
= 9960. Å		10 Å/pix.
x 708 pix.
= 7080. 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: 10 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.30429697 - 0.20673603
Average (Standard dev.)-0.000000000000639 (±0.025619878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions996708518
Spacing708996518
CellA: 7080.0 Å / B: 9960.0 Å / C: 5180.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Goslar infected chmA KD E. coli cell 30 mpi

EntireName: Goslar infected chmA KD E. coli cell 30 mpi
Components
  • Cell: Goslar infected chmA KD E. coli cell 30 mpi

-
Supramolecule #1: Goslar infected chmA KD E. coli cell 30 mpi

SupramoleculeName: Goslar infected chmA KD E. coli cell 30 mpi / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 78 K / Focused ion beam - Initial thickness: 300 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2 dual beam microscope. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 4.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Software - Name: Warp (ver. 1.1.0) / Number images used: 37

+
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