[English] 日本語
Yorodumi
- PDB-8w9q: Structure of partial Banna virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w9q
TitleStructure of partial Banna virus
Components
  • VP10
  • VP2
  • VP4
  • VP8
  • VP9
KeywordsVIRUS / reovirus / intermediate state / capsid protein / complex
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Seadornavirus VP4 protein / Outer capsid protein VP9/VP10/VP11 / Outer capsid protein VP9, N-terminal / Reoviridae VP9 / Structural protein Vp10, Seadornavirus / Seadornavirus VP8 protein / Seadornavirus Vp10 / Seadornavirus VP2 protein
Similarity search - Domain/homology
VP10 / VP4 / Vp2 / VP9 / VP8
Similarity search - Component
Biological speciesBanna virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsLi, Z. / Cao, S.
Funding support China, 1items
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
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP2
B: VP2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
R: VP4
S: VP4
T: VP4
r: VP9
s: VP9
t: VP9


Theoretical massNumber of molelcules
Total (without water)1,001,92923
Polymers1,001,92923
Non-polymers00
Water00
1
A: VP2
B: VP2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
R: VP4
S: VP4
T: VP4
r: VP9
s: VP9
t: VP9
x 60


Theoretical massNumber of molelcules
Total (without water)60,115,7131380
Polymers60,115,7131380
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP2
B: VP2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
R: VP4
S: VP4
T: VP4
r: VP9
s: VP9
t: VP9
x 5


  • icosahedral pentamer
  • 5.01 MDa, 115 polymers
Theoretical massNumber of molelcules
Total (without water)5,009,643115
Polymers5,009,643115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP2
B: VP2
C: VP8
D: VP8
E: VP8
F: VP8
G: VP8
H: VP8
I: VP8
J: VP8
K: VP8
L: VP8
M: VP8
N: VP8
O: VP8
P: VP10
Q: VP10
R: VP4
S: VP4
T: VP4
r: VP9
s: VP9
t: VP9
x 6


  • icosahedral 23 hexamer
  • 6.01 MDa, 138 polymers
Theoretical massNumber of molelcules
Total (without water)6,011,571138
Polymers6,011,571138
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein VP2


Mass: 108031.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OR004519 / Source: (natural) Banna virus / References: UniProt: Q9INH3
#2: Protein
VP8


Mass: 32885.305 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Details: OR004525 / Source: (natural) Banna virus / References: UniProt: W0G587
#3: Protein VP10


Mass: 28655.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OR004527 / Source: (natural) Banna virus / References: UniProt: A0A2H4QDD3
#4: Protein VP4


Mass: 69767.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: OR004521 / Source: (natural) Banna virus / References: UniProt: B4Y048
#5: Protein VP9


Mass: 30581.178 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: OR004526 / Source: (natural) Banna virus / References: UniProt: Q9YWN5

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Banna virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Banna virus / Strain: YN15-126-01
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
4RELION3.1.1CTF correction
13RELION3.1.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13225 / Symmetry type: POINT

+
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