[English] 日本語
Yorodumi
- PDB-9ffg: Empty capsid of Rhodobacter microvirus Ebor computed with I4 symmetry -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ffg
TitleEmpty capsid of Rhodobacter microvirus Ebor computed with I4 symmetry
ComponentsMajor capsid protein
KeywordsVIRUS / ssDNA virus / Microviridae / Tainavirinae / Alphaproteobacteria / Rhodobacter capsulatus / aquatic virus / jelly-roll fold
Biological speciesRhodobacter capsulatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBardy, P. / MacDonald, C.I.W. / Jenkins, H.T. / Byrom, L. / Chechik, M. / Hart, S.J. / Turkenburg, J.P. / Blaza, J.N. / Fogg, P.C.M. / Antson, A.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust224067/Z/21/Z United Kingdom
Wellcome Trust206377 United Kingdom
Wellcome Trust109363/Z/15/A United Kingdom
CitationJournal: bioRxiv / Year: 2024
Title: A stargate mechanism of genome delivery unveiled by cryogenic electron tomography.
Authors: Pavol Bardy / Conor I W MacDonald / Paul C Kirchberger / Huw T Jenkins / Tibor Botka / Lewis Byrom / Nawshin T B Alim / Daouda A K Traore / Hannah C König / Tristan R Nicholas / Maria ...Authors: Pavol Bardy / Conor I W MacDonald / Paul C Kirchberger / Huw T Jenkins / Tibor Botka / Lewis Byrom / Nawshin T B Alim / Daouda A K Traore / Hannah C König / Tristan R Nicholas / Maria Chechik / Samuel J Hart / Johan P Turkenburg / James N Blaza / J Thomas Beatty / Paul C M Fogg / Alfred A Antson /
Abstract: Single-stranded DNA bacteriophages of the family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut ...Single-stranded DNA bacteriophages of the family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.
History
DepositionMay 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)55,8151
Polymers55,8151
Non-polymers00
Water00
1
A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein

A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)3,348,92560
Polymers3,348,92560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

-
Components

#1: Protein Major capsid protein


Mass: 55815.418 Da / Num. of mol.: 1 / Mutation: variant S120 / Source method: isolated from a natural source / Details: Ebor variant S120 / Source: (natural) Rhodobacter capsulatus (bacteria) / Strain: B10

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Rhodobacter phage Ebor / Type: VIRUS
Details: purified from Rhodobacter capsulatus strain B10 by sucrose ultracentrifugation
Entity ID: all / Source: NATURAL
Molecular weightValue: 3.68 MDa / Experimental value: NO
Source (natural)Organism: Rhodobacter phage Ebor (virus) / Strain: variant S120
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Rhodobacter capsulatus / Strain: B10
Virus shellName: Empty capsid / Diameter: 280 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.75
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
2100 mMsodium chlorideNaCl1
35 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: concentration of 5x10^10 PFU/ml
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K / Details: blot time 2 sec, blot force 0, wait time 8 sec

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1099

-
Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.9.8.5model fitting
9PHENIX1.20.1model refinement
10RELION3.1.initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3976
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1984 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00234470
ELECTRON MICROSCOPYf_angle_d0.47446980
ELECTRON MICROSCOPYf_dihedral_angle_d11.12312910
ELECTRON MICROSCOPYf_chiral_restr0.0485460
ELECTRON MICROSCOPYf_plane_restr0.0046190

+
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