[English] 日本語
Yorodumi
- EMDB-43722: Cryo-EM structure of pre-subcore from in vitro assembled particles -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43722
TitleCryo-EM structure of pre-subcore from in vitro assembled particles
Map data
Sample
  • Virus: Bluetongue virus (serotype 1 / isolate South Africa)
    • Protein or peptide: inner capsid protein VP3
    • Protein or peptide: inner capsid protein VP6
KeywordsBluetongue virus / capsid protein / assembly intermediate / virial proteins / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


virion component / viral capsid / structural molecule activity
Similarity search - Function
VP6 blue-tongue virus inner capsid protein / Orbivirus helicase VP6 / Inner layer core protein VP3, Orbivirus / Orbivirus VP3 (T2) protein / Inner layer core protein VP3, Reovirus
Similarity search - Domain/homology
VP6 / Core protein VP3
Similarity search - Component
Biological speciesBluetongue virus (serotype 1 / isolate South Africa)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXia X / Sung PY / Martynowycz MW / Gonen T / Roy P / Zhou ZH
Funding support United States, United Kingdom, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
Wellcome TrustWT221749/20/Z United Kingdom
CitationJournal: Cell / Year: 2024
Title: RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells.
Authors: Xian Xia / Po-Yu Sung / Michael W Martynowycz / Tamir Gonen / Polly Roy / Z Hong Zhou /
Abstract: Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques ...Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.
History
DepositionFeb 15, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43722.png

Downloads & links

-
Map

FileDownload / File: emd_43722.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0013480434 - 1.9717581
Average (Standard dev.)0.015472153 (±0.09898997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_43722_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43722_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bluetongue virus (serotype 1 / isolate South Africa)

EntireName: Bluetongue virus (serotype 1 / isolate South Africa)
Components
  • Virus: Bluetongue virus (serotype 1 / isolate South Africa)
    • Protein or peptide: inner capsid protein VP3
    • Protein or peptide: inner capsid protein VP6

-
Supramolecule #1: Bluetongue virus (serotype 1 / isolate South Africa)

SupramoleculeName: Bluetongue virus (serotype 1 / isolate South Africa) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10905
Sci species name: Bluetongue virus (serotype 1 / isolate South Africa)
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Ovis aries (sheep)

-
Macromolecule #1: inner capsid protein VP3

MacromoleculeName: inner capsid protein VP3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSISF RHIVMQSRDR VLRVDTYYEE MSQVGDVITE DEPEKFYSTI IKKVRFIRGK GSFILHDIPT RDHRGMEVAE PEVLGVEFKN ...String:
MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSISF RHIVMQSRDR VLRVDTYYEE MSQVGDVITE DEPEKFYSTI IKKVRFIRGK GSFILHDIPT RDHRGMEVAE PEVLGVEFKN VLPVLTAEHR AMIQNALDGS IIENGNVATR DVDVFIGACS EPVYRIYNRL QGYIEAVQLQ ELRNSIGWLE RLGHRKRITY SQEVLTDFRR QDTIWVLALQ LPVNPQVVWD VPRSSIANLI MNIATCLPTG EYIAPNPRIS SITLTQRITT TGPFAILTGS TPTAQQLNDV RKIYLALMFP GQIILDLKID PGERMDPAVR MVAGVVGHLL FTAGGRFTNL TQNMARQLDI ALNDYLLYMY NTRVQVNYGP TGEPLDFQIG RNQYDCNVFR ADFATGTGYN GWATIDVEYR EPAPYVHAQR YIRYCGIDSR ELINPTTYGI GMTYHCYNEM LRMLVAAGKD SEAAYFRSML PFHMVRFARI NQIINEDLHS VFSLPDDMFN ALLPDLIAGA HQNADPVVLD VSWISLWFAF NRSFEPTHRN EMLEVAPLIE SVYASELSVM KVDMRHLSLM QRRFPDVLIQ ARPSHFWKAV LNDSPEAVKA VMNLSHSHNF INIRDMMRWV MLPSLQPSLK LALEEEAWAA ANDFEDLMLT DQVYMHRDML PEPRLDDIER FRQEGFYYTN MLEAPPEIDR VVQYTYEIAR LQANMGQFRA ALRRIMDDDD WVRFGGVLRT VRVKFYDARP PDDVLQGLPF SYDTNERGGL AYATIKYATE TTIFYLIYNV EFSNTPDSLV LINPTYTMTK VFINKRIVER VRVGQILAVL NRRFVAYKGK MRIMDITQSL KMGTKLAAPT V

UniProtKB: Core protein VP3

-
Macromolecule #2: inner capsid protein VP6

MacromoleculeName: inner capsid protein VP6 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)
SequenceString: MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSESSQKKES SKETKDADVD RRIHTAVGSG SSAKGPGERA NENVDRGDGK VGGGGGDADA GVGATGANGG RWVVLTEEIA RAIESKYGTK IDVYRDEVPA QIIEVERSLQ ...String:
MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSESSQKKES SKETKDADVD RRIHTAVGSG SSAKGPGERA NENVDRGDGK VGGGGGDADA GVGATGANGG RWVVLTEEIA RAIESKYGTK IDVYRDEVPA QIIEVERSLQ KELGISREGV AEQTERLRDL RRKEKSGAHA KAAERGRRKQ GKKPHGDAQR EGTEEEKTSE EPASVGITIE GVMSQKKLLS MIGGVERKMA PIGARESAVM LVSNSIKDVV RATAYFTAPT GDPHWKEVAR EASKKKNILA YTSTGGDVKT EFLHLIDHL

UniProtKB: VP6

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
10.0 mMTris
100.0 mMSodium ChlorideNaCl
1.0 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsIn vitro assembled capsid by using the purified proteins

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9015 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 64032
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 17277
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 20000 / Software - Name: RELION (ver. 3.1)

+
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