[English] 日本語
Yorodumi
- EMDB-16687: Carin1 bacteriophage mature capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16687
TitleCarin1 bacteriophage mature capsid
Map data
SampleBacteriophage sp. Cobetia Marina Virus Carin1 != Bacteriophage sp.

Bacteriophage sp. Cobetia Marina Virus Carin1

  • Virus: Bacteriophage sp. (virus)
    • Protein or peptide: Major Capsid Protein
    • Protein or peptide: Spike Base Protein
    • Protein or peptide: Capsid Decoration Protein
Biological speciesBacteriophage sp. (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
Authorsd'Acapito A / Neumann E / Schoehn G
Funding support France, 1 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: J Virol / Year: 2023
Title: Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM.
Authors: Alessio d'Acapito / Thomas Roret / Eleftherios Zarkadas / Pierre-Yves Mocaër / Florian Lelchat / Anne-Claire Baudoux / Guy Schoehn / Emmanuelle Neumann /
Abstract: Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely ...Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina (Carin-1) is a member of the family infecting the γ. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem.
History
DepositionFeb 14, 2023-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16687.png

Downloads & links

-
Map

FileDownload / File: emd_16687.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.728 Å
Density
Contour LevelBy AUTHOR: 0.0209
Minimum - Maximum-0.042207353 - 0.08579322
Average (Standard dev.)0.0003273031 (±0.0036225498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1382.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_16687_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16687_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacteriophage sp. Cobetia Marina Virus Carin1

EntireName: Bacteriophage sp. Cobetia Marina Virus Carin1
Components
  • Virus: Bacteriophage sp. (virus)
    • Protein or peptide: Major Capsid Protein
    • Protein or peptide: Spike Base Protein
    • Protein or peptide: Capsid Decoration Protein

-
Supramolecule #1: Bacteriophage sp.

SupramoleculeName: Bacteriophage sp. / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cobetia Marina Virus 1 / NCBI-ID: 3801 / Sci species name: Bacteriophage sp. / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Cobetia marina (bacteria) / Strain: DSM 4741
Virus shellShell ID: 1 / Name: Icosahedral capsid / Diameter: 700.0 Å / T number (triangulation number): 7

-
Macromolecule #1: Major Capsid Protein

MacromoleculeName: Major Capsid Protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage sp. (virus)
Molecular weightTheoretical: 37.781699 KDa
SequenceString: MATLGNTYLT LADVQKQKDG KGNVTSEIIE MLAETNPILE DMVVMECNDG TGHLTTIRTG LPQATWRRLY EGVQPAKSTT RQIKDSTGT LEAWSEVDEK LVKLSKDKQQ LMLNEAAAFL EGMNQTMAST LFYGNTATDA VKFMGLAPRF NAYRAARNLK P VDTADQVI ...String:
MATLGNTYLT LADVQKQKDG KGNVTSEIIE MLAETNPILE DMVVMECNDG TGHLTTIRTG LPQATWRRLY EGVQPAKSTT RQIKDSTGT LEAWSEVDEK LVKLSKDKQQ LMLNEAAAFL EGMNQTMAST LFYGNTATDA VKFMGLAPRF NAYRAARNLK P VDTADQVI DAGGTGSDLT SIWMVVWGDR TAHGLYPEGT SAGLQREYLG AETKELGDGG VYRVVREKFE WDLGLTVRDF RY VVRIANI DVSDLQAGTI DIYALLRKAY YRLENRVITG GRAALYCNAD VTEAMDAAAT PTSSTTASYV RLTPMQVDGK EVM MYRGIP VRECDAILST ETAVPSVA

-
Macromolecule #2: Spike Base Protein

MacromoleculeName: Spike Base Protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage sp. (virus)
Molecular weightTheoretical: 9.510708 KDa
SequenceString:
MAIGDIQTSV AFDRQVGRFP PRAEVVTPSN SEEFTSGVSV FSNDGGDISV VPLLPYGSAA IVVTVAAGGF VPFMVRKVNA TGTTSTSIV AVW

-
Macromolecule #3: Capsid Decoration Protein

MacromoleculeName: Capsid Decoration Protein / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage sp. (virus)
Molecular weightTheoretical: 13.581196 KDa
SequenceString:
MIMDKENTFS YKQAITGTAV STNVIDLGVS RDIGKGVPVP IIIQVVEDFA DATSLTATLQ TSETENFSSA TTLATSGAVP VADLTAGKQ LAVQYMPLGT QRYLRVNYTV SGTATAGAVT AGVVMSHQQN D

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Component - Concentration: 1.0 x / Component - Name: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 25mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 56972
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

+
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