[English] 日本語
Yorodumi
- EMDB-28605: Acheta domesticus segmented densovirus high buoyancy fraction 1 (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28605
TitleAcheta domesticus segmented densovirus high buoyancy fraction 1 (HB1) empty capsid structure
Map dataAcheta domesticus segmented densovirus high buoyancy fraction 1 (HB1) empty capsid structure
Sample
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Capsid protein
Keywordsparvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus / VIRUS LIKE PARTICLE
Function / homologyCapsid protein
Function and homology information
Biological speciesSolenopsis invicta-associated densovirus / unclassified Densovirinae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPenzes JJ / McKenna R / Tijssen P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Nat Commun / Year: 2023
Title: Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus.
Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Emmanuel W Smith / Robert McKenna / Peter Tijssen /
Abstract: Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression ...Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
History
DepositionOct 18, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28605.png

Downloads & links

-
Map

FileDownload / File: emd_28605.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcheta domesticus segmented densovirus high buoyancy fraction 1 (HB1) empty capsid structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 500 pix.
= 529.5 Å		1.06 Å/pix.
x 500 pix.
= 529.5 Å		1.06 Å/pix.
x 500 pix.
= 529.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-15.461636 - 27.378525
Average (Standard dev.)-0.000000001366577 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 529.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : unclassified Densovirinae

EntireName: unclassified Densovirinae (virus)
Components
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Capsid protein

-
Supramolecule #1: unclassified Densovirinae

SupramoleculeName: unclassified Densovirinae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 185880 / Sci species name: unclassified Densovirinae / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Acheta domesticus (house cricket)

-
Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Solenopsis invicta-associated densovirus
Molecular weightTheoretical: 36.291906 KDa
Recombinant expressionOrganism: Acheta domesticus (house cricket)
SequenceString: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP ...String:
EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP TREKWCHTWD LDVLNHNYLW EPNNLDSQWT LIPGAQAVQP TATPIGPTYQ EIVIATKAIG ANESALVTTI QD RRSYPRL MLSQPQIKDE TDTMKFKYQI RISTELEMEH HIKPDIANPW LTRQTLPLPA LSGDGTTRYV PCVPYETHVS Q

UniProtKB: Capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 x / Component - Name: Phosphate buffered saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
DetailsDeceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 970 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.81 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 46082
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio random model based on 100 boxed particles
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 30065
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cisTEM (ver. 1.0.0)
Final 3D classificationNumber classes: 30 / Software - Name: cisTEM (ver. 1.0.0)

+
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