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- EMDB-34213: Complex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125 -

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Basic information

Entry
Database: EMDB / ID: EMD-34213
TitleComplex of FMDV A/WH/CHA/09 and bovine neutralizing scFv antibody W125
Map data
Sample
  • Complex: Foot-and-mouth disease virus
    • Complex: Foot-and-mouth disease virus
      • Protein or peptide: A/WH/CHA/09 VP1
      • Protein or peptide: A/WH/CHA/09 VP2
      • Protein or peptide: A/WH/CHA/09 VP3
      • Protein or peptide: A/WH/CHA/09 VP4
    • Complex: Ig chain
      • Protein or peptide: IG HEAVY CHAIN VARIABLE REGION
      • Protein or peptide: IG LAMDA CHAIN VARIABLE REGION
KeywordsFOOT AND MOUTH DISEASE VIRUS / FMDV / VIRUS
Function / homology
Function and homology information


icosahedral viral capsid / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / channel activity / regulation of translation / monoatomic ion transmembrane transport ...icosahedral viral capsid / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / 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 / cytoplasm
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
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus A / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsHe Y / Kun L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2023
Title: Conserved antigen structures and antibody-driven variations on foot-and-mouth disease virus serotype A revealed by bovine neutralizing monoclonal antibodies.
Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Huifang Bao / Shulun Huang / Shasha Zhou / Guoqiang Zhu / Yali Song / Ying Li / Sheng Wang / Qianliang Zhang / Pu Sun / Xingwen Bai / Zhixun Zhao / ...Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Huifang Bao / Shulun Huang / Shasha Zhou / Guoqiang Zhu / Yali Song / Ying Li / Sheng Wang / Qianliang Zhang / Pu Sun / Xingwen Bai / Zhixun Zhao / Zhiyong Lou / Yimei Cao / Zengjun Lu / Zaixin Liu /
Abstract: Foot-and-mouth disease virus (FMDV) serotype A is antigenically most variable within serotypes. The structures of conserved and variable antigenic sites were not well resolved. Here, a historical ...Foot-and-mouth disease virus (FMDV) serotype A is antigenically most variable within serotypes. The structures of conserved and variable antigenic sites were not well resolved. Here, a historical A/AF72 strain from A22 lineage and a latest A/GDMM/2013 strain from G2 genotype of Sea97 lineage were respectively used as bait antigen to screen single B cell antibodies from bovine sequentially vaccinated with A/WH/CHA/09 (G1 genotype of Sea97 lineage), A/GDMM/2013 and A/AF72 antigens. Total of 39 strain-specific and 5 broad neutralizing antibodies (bnAbs) were isolated and characterized. Two conserved antigenic sites were revealed by the Cryo-EM structures of FMDV serotype A with two bnAbs W2 and W125. The contact sites with both VH and VL of W125 were closely around icosahedral threefold axis and covered the B-C, E-F, and H-I loops on VP2 and the B-B knob and H-I loop on VP3; while contact sites with only VH of W2 concentrated on B-B knob, B-C and E-F loops on VP3 scattering around the three-fold axis of viral particle. Additional highly conserved epitopes also involved key residues of VP158, VP1147 and both VP272 / VP1147 as determined respectively by bnAb W153, W145 and W151-resistant mutants. Furthermore, the epitopes recognized by 20 strain-specific neutralization antibodies involved the key residues located on VP3 68 for A/AF72 (11/20) and VP3 175 position for A/GDMM/2013 (9/19), respectively, which revealed antigenic variation between different strains of serotype A. Analysis of antibody-driven variations on capsid of two virus strains showed a relatively stable VP2 and more variable VP3 and VP1. This study provided important information on conserve and variable antigen structures to design broad-spectrum molecular vaccine against FMDV serotype A.
History
DepositionSep 2, 2022-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34213.png

Downloads & links

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Map

FileDownload / File: emd_34213.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0773446 - 0.12024331
Average (Standard dev.)0.0012102034 (±0.007871627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-239-239-239
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34213_half_map_1.map
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Half map: #1

Fileemd_34213_half_map_2.map
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Sample components

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Entire : Foot-and-mouth disease virus

EntireName: Foot-and-mouth disease virus
Components
  • Complex: Foot-and-mouth disease virus
    • Complex: Foot-and-mouth disease virus
      • Protein or peptide: A/WH/CHA/09 VP1
      • Protein or peptide: A/WH/CHA/09 VP2
      • Protein or peptide: A/WH/CHA/09 VP3
      • Protein or peptide: A/WH/CHA/09 VP4
    • Complex: Ig chain
      • Protein or peptide: IG HEAVY CHAIN VARIABLE REGION
      • Protein or peptide: IG LAMDA CHAIN VARIABLE REGION

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Supramolecule #1: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Foot-and-mouth disease virus A

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Supramolecule #3: Ig chain

SupramoleculeName: Ig chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: A/WH/CHA/09 VP1

MacromoleculeName: A/WH/CHA/09 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 23.402678 KDa
SequenceString: TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA ...String:
TTATGESADP VTTTVENYGG ETQVQRRHHT DVSFIMDRFV QIKPVSPTHV IDLMQTHQHG LVGAMLRAAT YYFSDLEIVV NHTGRLTWV PNGAPEAALD NTSNPTAYHK APFTRLALPY TAPHRVLATV YNGNSKYSAP ATRRGDLGSL AARLAAQLPA S FNYGAIRA TEIQELLVRM KRAELYCPRP LLAVKVTSQD RHKQKIIAPA KQLL

UniProtKB: Genome polyprotein

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Macromolecule #2: A/WH/CHA/09 VP2

MacromoleculeName: A/WH/CHA/09 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 24.541584 KDa
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVVQAER FFKKHLFDWT TDKPFGHIEK LELPTDHKG VYGQLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEF KEFTTREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYNKHKPWT LVVMVVSPLT TSSIGASQIK VYTNIAPTHV HVAGELPSKE

UniProtKB: Genome polyprotein

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Macromolecule #3: A/WH/CHA/09 VP3

MacromoleculeName: A/WH/CHA/09 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 24.157025 KDa
SequenceString: GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String:
GIVPVACSDG YGGLVTTDPK TADPAYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADE QRLLAKFDLS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VTTPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVADT TNVQGWVCIY QITHGKAEQD TLVVSVSAGK DFELRLPIDP RAQ

UniProtKB: Genome polyprotein

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Macromolecule #4: A/WH/CHA/09 VP4

MacromoleculeName: A/WH/CHA/09 VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 8.778129 KDa
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSSHTT NTQNNDWFSK LASSAFTGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: IG HEAVY CHAIN VARIABLE REGION

MacromoleculeName: IG HEAVY CHAIN VARIABLE REGION / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 14.60416 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLRESGPS LVKPSQTLSL TCTVSGFSLS TYAVYWVRQA PGKALECLGS VSSGDYLTYN PALKSRLTIT KDNSKSEVSL SVSTVTPED TATYYCAKSH SSGYNGWIDF GCYEFTGYGP RYVDAWGQGV QVTVSS

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Macromolecule #6: IG LAMDA CHAIN VARIABLE REGION

MacromoleculeName: IG LAMDA CHAIN VARIABLE REGION / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 12.701598 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
WAQAVLTQPS SVSGSLGQRV SITCSGSSSN VGLGNYVSWF QQIPGSAPRT LIYGATNQAS GVPDRFSGSR SGNTATLTIS SLQAEDEAN YFCASPDSSQ TIFGSGTTLT VLGDYKDDDD DKGG

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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: FEI FALCON II (4k x 4k) / Average electron dose: 26.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12646
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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