[English] 日本語
Yorodumi
- EMDB-36872: Structure of VP9 in Banna virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36872
TitleStructure of VP9 in Banna virus
Map data
Sample
  • Virus: Banna virus
    • Protein or peptide: VP9
Keywordsreceptor binding / spike / reovirus / VIRAL PROTEIN
Function / homologyOuter capsid protein VP9/VP10/VP11 / Outer capsid protein VP9, N-terminal / Reoviridae VP9 / identical protein binding / VP9
Function and homology information
Biological speciesBanna virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi Z / Cao S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes.
Authors: Zhiqiang Li / Han Xia / Guibo Rao / Yan Fu / Tingting Chong / Kexing Tian / Zhiming Yuan / Sheng Cao /
Abstract: Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions- ...Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions-surrounded by 120 spikes (full virions), 60 spikes (partial virions), or no spikes (cores). BAV cores are double-layered particles similar to the cores of other non-turreted reoviruses, except for an additional protein component in the outer capsid shell, VP10. VP10 was identified to be a cementing protein that plays a pivotal role in the assembly of BAV virions by directly interacting with VP2 (inner capsid), VP8 (outer capsid), and VP4 (spike). Viral spikes (VP4/VP9 heterohexamers) are situated on top of VP10 molecules in full or partial virions. Asymmetrical electrostatic interactions between VP10 monomers and VP4 trimers are disrupted by high pH treatment, which is thus a simple way to produce BAV cores. Low pH treatment of BAV virions removes only the flexible receptor binding protein VP9 and triggers significant conformational changes in the membrane penetration protein VP4. BAV virions adopt distinct spatial organization of their surface proteins compared with other well-studied reoviruses, suggesting that BAV may have a unique mechanism of penetration of cellular endomembranes.
History
DepositionJul 17, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36872.png

Downloads & links

-
Map

FileDownload / File: emd_36872.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 180 pix.
= 171. Å		0.95 Å/pix.
x 180 pix.
= 171. Å		0.95 Å/pix.
x 180 pix.
= 171. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.6747807 - 0.9975674
Average (Standard dev.)0.0017324559 (±0.056755293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 171.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36872_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Banna virus

EntireName: Banna virus
Components
  • Virus: Banna virus
    • Protein or peptide: VP9

-
Supramolecule #1: Banna virus

SupramoleculeName: Banna virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 77763 / Sci species name: Banna virus / Sci species strain: YN15-126-01 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: VP9

MacromoleculeName: VP9 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 30.581178 KDa
SequenceString: MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT ...String:
MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT SLSTTASSTN SFAYSTCSVP IENWDFNMIK LTAETSCASL TAMTNLVNSL VPGERTRPVG LYVDIPGVTV TT SASSGSL PLTTIPAVTP LIFSAYTKQV EEVGVINTLY ALSYLP

UniProtKB: VP9

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 443253
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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://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