[English] 日本語
Yorodumi
- PDB-7eno: Mutant strain M3 of foot-and-mouth disease virus type O -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eno
TitleMutant strain M3 of foot-and-mouth disease virus type O
Components
  • VP1 of O type FMDV capsid
  • VP2 of O type FMDV capsid
  • VP3 of O type FMDV capsid
  • VP4 of O type FMDV capsid
KeywordsVIRUS / FMDV
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : ...L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus - type O
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsDong, H. / Lu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31941011, 12034006 China
CitationJournal: J Virol / Year: 2021
Title: A Heat-Induced Mutation on VP1 of Foot-and-Mouth Disease Virus Serotype O Enhanced Capsid Stability and Immunogenicity.
Authors: Hu Dong / Yuanlu Lu / Yun Zhang / Suyu Mu / Nan Wang / Ping Du / Xiaoying Zhi / Xiaobo Wen / Xiangxi Wang / Shiqi Sun / Yanming Zhang / Huichen Guo /
Abstract: Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes a significant economic burden globally. Vaccination is the most effective FMD control ...Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals that causes a significant economic burden globally. Vaccination is the most effective FMD control strategy. However, FMD virus (FMDV) particles are prone to dissociate when appropriate physical or chemical conditions are unavailable, such as an incomplete cold chain. Such degraded vaccines result in compromised herd vaccination. Therefore, thermostable FMD particles are needed for use in vaccines. This study generated thermostable FMDV mutants (M3 and M10) by serial passages at high temperature, subsequent amplification, and purification. Both mutants contained an alanine-to-threonine mutation at position 13 in VP1 (A1013T), although M3 contained 3 additional mutations. The selected mutants showed improved stability and immunogenicity in neutralizing antibody titers, compared with the wild-type (wt) virus. The sequencing analysis and cryo-electron microscopy showed that the mutation of alanine to threonine at the 13th amino acid in the VP1 protein (A1013T) is critical for the capsid stability of FMDV. Virus-like particles containing A1013T (VLP) also showed significantly improved stability to heat treatment. This study demonstrated that Thr at the 13th amino acid of VP1 could stabilize the capsid of FMDV. Our findings will facilitate the development of a stable vaccine against FMDV serotype O. Foot-and-mouth disease (FMD) serotype O is one of the global epidemic serotypes and causes significant economic loss. Vaccination plays a key role in the prevention and control of FMD. However, the success of vaccination mainly depends on the quality of the vaccine. Here, the thermostable FMD virus (FMDV) mutants (M3 and M10) were selected through thermal screening at high temperatures with improved stability and immunogenicity compared with the wild-type virus. The results of multisequence alignment and cryo-electron microscopy (cryo-EM) analysis showed that the Thr substitution at the 13th amino acid in the VP1 protein is critical for the capsid stability of FMDV. For thermolabile type O FMDV, this major discovery will aid the development of its thermostable vaccine.
History
DepositionApr 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Oct 13, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.4Oct 20, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.5Oct 27, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.6Dec 1, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.7Dec 8, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.8Jan 26, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-31218
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-31218
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: VP1 of O type FMDV capsid
2: VP2 of O type FMDV capsid
3: VP3 of O type FMDV capsid
4: VP4 of O type FMDV capsid


Theoretical massNumber of molelcules
Total (without water)80,4194
Polymers80,4194
Non-polymers00
Water0
1
1: VP1 of O type FMDV capsid
2: VP2 of O type FMDV capsid
3: VP3 of O type FMDV capsid
4: VP4 of O type FMDV capsid
x 60


Theoretical massNumber of molelcules
Total (without water)4,825,150240
Polymers4,825,150240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: VP1 of O type FMDV capsid
2: VP2 of O type FMDV capsid
3: VP3 of O type FMDV capsid
4: VP4 of O type FMDV capsid
x 5


  • icosahedral pentamer
  • 402 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)402,09620
Polymers402,09620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1 of O type FMDV capsid
2: VP2 of O type FMDV capsid
3: VP3 of O type FMDV capsid
4: VP4 of O type FMDV capsid
x 6


  • icosahedral 23 hexamer
  • 483 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)482,51524
Polymers482,51524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: VP1 of O type FMDV capsid
2: VP2 of O type FMDV capsid
3: VP3 of O type FMDV capsid
4: VP4 of O type FMDV capsid
x 60


  • crystal asymmetric unit, crystal frame
  • 4.83 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,825,150240
Polymers4,825,150240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein VP1 of O type FMDV capsid


Mass: 23247.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Escherichia coli (E. coli)
#2: Protein VP2 of O type FMDV capsid


Mass: 24510.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Escherichia coli (E. coli)
#3: Protein VP3 of O type FMDV capsid


Mass: 23882.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Escherichia coli (E. coli)
#4: Protein VP4 of O type FMDV capsid


Mass: 8778.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Escherichia coli (E. coli) / References: UniProt: L0AP64

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Foot-and-mouth disease virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Foot-and-mouth disease virus - type O
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055228
ELECTRON MICROSCOPYf_angle_d0.637138
ELECTRON MICROSCOPYf_dihedral_angle_d5.506708
ELECTRON MICROSCOPYf_chiral_restr0.044808
ELECTRON MICROSCOPYf_plane_restr0.005921

+
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