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- EMDB-31218: Mutant strain M3 of foot-and-mouth disease virus type O -

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Basic information

Entry
Database: EMDB / ID: EMD-31218
TitleMutant strain M3 of foot-and-mouth disease virus type O
Map data
SampleFoot-and-mouth disease virus != Foot-and-mouth disease virus - type O

Foot-and-mouth disease virus

  • Virus: Foot-and-mouth disease virus - type O
    • Protein or peptide: VP1 of O type FMDV capsid
    • Protein or peptide: VP2 of O type FMDV capsid
    • Protein or peptide: VP3 of O type FMDV capsid
    • Protein or peptide: VP4 of O type FMDV capsid
KeywordsFMDV / VIRUS
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsDong H / Lu Y
Funding support China, 1 items
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, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-7eno
  • Surface level: 0.03
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eno
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31218.png

Downloads & links

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Map

FileDownload / File: emd_31218.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.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.090838 - 0.14368623
Average (Standard dev.)0.0014273231 (±0.009740202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0910.1440.001

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Supplemental data

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Sample components

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Entire : Foot-and-mouth disease virus

EntireName: Foot-and-mouth disease virus
Components
  • Virus: Foot-and-mouth disease virus - type O
    • Protein or peptide: VP1 of O type FMDV capsid
    • Protein or peptide: VP2 of O type FMDV capsid
    • Protein or peptide: VP3 of O type FMDV capsid
    • Protein or peptide: VP4 of O type FMDV capsid

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Supramolecule #1: Foot-and-mouth disease virus - type O

SupramoleculeName: Foot-and-mouth disease virus - type O / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12118 / Sci species name: Foot-and-mouth disease virus - type O / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP1 of O type FMDV capsid

MacromoleculeName: VP1 of O type FMDV capsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus - type O
Molecular weightTheoretical: 23.247596 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TTSTGESADP VTTTVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGECKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI ...String:
TTSTGESADP VTTTVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGECKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI KATRVIELLY RMKRAETYCP RPLLAVHPSA ARHKQKIVAP VKQ

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Macromolecule #2: VP2 of O type FMDV capsid

MacromoleculeName: VP2 of O type FMDV capsid / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus - type O
Molecular weightTheoretical: 24.510613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GITHGYATAE DFVNGPNTSG LETRVIQAER FFKTHLFDWV TSDPFGRYYL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIEQRELFQ LTLFPHQFIN PRTNMTAHIK V PFVGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GITHGYATAE DFVNGPNTSG LETRVIQAER FFKTHLFDWV TSDPFGRYYL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIEQRELFQ LTLFPHQFIN PRTNMTAHIK V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNTEGAPQIK VYANIAPTNV HVAGEFPSKE

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Macromolecule #3: VP3 of O type FMDV capsid

MacromoleculeName: VP3 of O type FMDV capsid / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus - type O
Molecular weightTheoretical: 23.882836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String:
GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDAAETT NVQGWVCLFQ ITHGKAEGDA LVVLASAGKD FELRLPVDAR QQ

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Macromolecule #4: VP4 of O type FMDV capsid

MacromoleculeName: VP4 of O type FMDV capsid / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus - type O
Molecular weightTheoretical: 8.778129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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