[English] 日本語
Yorodumi
- EMDB-51613: Giant Jyvaskylavirus at 6.3 Ang resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51613
TitleGiant Jyvaskylavirus at 6.3 Ang resolution
Map dataIMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Post-processed map, no masked, using the automatic B-factor sharpening by RELION.
Sample
  • Virus: Jyvaskylavirus
    • Other: Jyvaskylavirus
KeywordsGiant virus / cryo-EM / genomic / NCLDV / Marseilleviridae family / VIRUS
Biological speciesAcanthamoeba castellanii (eukaryote) / Jyvaskylavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsAbrescia NG / Arriaga I / de Freitas Almeida GM / Sundberg LR / Ravantti J
Funding support Spain, Finland, Norway, United Kingdom, 6 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-126130OB-I00 Spain
Academy of Finlandgrant #314939 Finland
Research Council of Norwayproject ID #2520855 Norway
Wellcome TrusteBIC access proposal CM30316 United Kingdom
Spanish Ministry of Science, Innovation, and Universitiesaccess RES BCV-2022-3-0015 Spain
Spanish Ministry of Science, Innovation, and UniversitiesCEX2021-001136-S Spain
CitationJournal: Elife / Year: 2025
Title: Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland.
Authors: Gabriel Magno de Freitas Almeida / Iker Arriaga / Bruna Luiza de Azevedo / Miika Leppänen / Jonatas S Abrahão / Julien Andreani / Davide Zabeo / Janne J Ravantti / Nicola G A Abrescia / ...Authors: Gabriel Magno de Freitas Almeida / Iker Arriaga / Bruna Luiza de Azevedo / Miika Leppänen / Jonatas S Abrahão / Julien Andreani / Davide Zabeo / Janne J Ravantti / Nicola G A Abrescia / Lotta-Riina Sundberg /
Abstract: Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found ...Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in from a composting soil sample in Jyväskylä, Central Finland. Its genome shares similarities with other marseilleviruses. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus life cycle. We reconstructed the Jyvaskylavirus particle to 6.3 Å resolution using cryo-electron microscopy. The ~2500 Å diameter virion displays structural similarities to other Marseilleviridae giant viruses. The capsid comprises of 9240 copies of the major capsid protein, encoded by open reading frame (ORF) 184, which possesses a double jellyroll fold arranged in trimers forming pseudo-hexameric capsomers. Below the capsid shell, the internal membrane vesicle encloses the genome. Through cross-structural and -sequence comparisons with other Marseilleviridae using AI-based software in model building and prediction, we elucidated ORF142 as the penton protein, which plugs the 12 vertices of the capsid. Five additional ORFs were identified, with models predicted and fitted into densities that either cap the capsomers externally or stabilize them internally. The isolation of Jyvaskylavirus suggests that these viruses may be widespread in the boreal environment and provide structural insights extendable to other marseilleviruses.
History
DepositionSep 20, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51613.png

Downloads & links

-
Map

FileDownload / File: emd_51613.map.gz / Format: CCP4 / Size: 5.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Post-processed map, no masked, using the automatic B-factor sharpening by RELION.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 2304 pix.
= 3087.36 Å		1.34 Å/pix.
x 2304 pix.
= 3087.36 Å		1.34 Å/pix.
x 2304 pix.
= 3087.36 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.00902783 - 0.020209888
Average (Standard dev.)0.0015317714 (±0.0023726863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230423042304
Spacing230423042304
CellA=B=C: 3087.36 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: IMPORTANT: Map has been binned from the original...

Fileemd_51613_half_map_1.map
AnnotationIMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Unfiltered, unmasked, half map 2 from the 3D auto refinement by RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: IMPORTANT: Map has been binned from the original...

Fileemd_51613_half_map_2.map
AnnotationIMPORTANT: Map has been binned from the original boxel size (1.34 A/px). Unfiltered, unmasked, half map 1 from the 3D auto refinement by RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Jyvaskylavirus

EntireName: Jyvaskylavirus
Components
  • Virus: Jyvaskylavirus
    • Other: Jyvaskylavirus

-
Supramolecule #1: Jyvaskylavirus

SupramoleculeName: Jyvaskylavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full virion / NCBI-ID: 1513458 / Sci species name: Jyvaskylavirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba castellanii (eukaryote)
Virus shellShell ID: 1 / Name: Jyvaskylavirus ORF184 / Diameter: 2500.0 Å / T number (triangulation number): 309

-
Macromolecule #1: Jyvaskylavirus

MacromoleculeName: Jyvaskylavirus / type: other / ID: 1 / Classification: other
Source (natural)Organism: Acanthamoeba castellanii (eukaryote)
SequenceString:
XXXXX

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
120.0 mg/LNaClsodium chloride
4.0 mg/LMgSO4magnesium sulfate
4.0 mg/LCaCl2calcium chloride
142.0 mg/LNa2HPO4disodium phosphate
136.0 mg/LKH2PO4monopotassium phosphate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 37 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa / Details: 8-9 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Also Automatic Plunge Freezer EM2 (Leica) was used (see publication)..

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 3742
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: integrative modelModelAngelo
source_name: Other, initial_model_type: integrative modelPlease see publication
DetailsPlease keep in mind that the predicted Jyvaskylavirus PDB models using ModelAngelo and Alphafold have been deposited at the Biostudies website (https://www.ebi.ac.uk/biostudies/). Please refer to the published article for the corresponding entry code.
RefinementProtocol: RIGID BODY FIT

+
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