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- EMDB-69004: Complex of FMDV O/18074 and porcine-derived neutralizing monoclon... -

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Basic information

Entry
Database: EMDB / ID: EMD-69004
TitleComplex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-29
Map data
Sample
  • Complex: Complex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-29
    • Complex: FMDV O/18074
      • Protein or peptide: VP1 of capsid protein
      • Protein or peptide: VP2 of capsid protein
      • Protein or peptide: VP3 of capsid protein
      • Protein or peptide: VP4 of capsid protein
    • Complex: porcine-derived neutralizing monoclonal antibody pO18-29
      • Protein or peptide: pO18-29 VH
      • Protein or peptide: pO18-29 VL
KeywordsFoot-and-mouth disease virus O / Sus scrofa / VIRUS/IMMUNE SYSTEM / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / viral capsid / ribonucleoside triphosphate phosphatase activity / host cell / host cell cytoplasm / viral protein processing / cysteine-type endopeptidase activity / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
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 superfamily, Picornavirus / Papain-like cysteine peptidase superfamily / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus O / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.34 Å
AuthorsWu S / Lei D
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171300 China
Other governmentR2405 China
National Natural Science Foundation of China (NSFC)32503058 China
National Natural Science Foundation of China (NSFC)32373028 China
Other governmentlzujbky-2021-ct05 China
Other government2021YFD1800304 China
Other governmentCAAS-CSLPDCP-202402 China
CitationJournal: Plos Pathog. / Year: 2026
Title: Structural basis of antigenic drift on FMDV O/Cathay topotype variants revealed by porcine-derived single B-cell neutralizing antibodies
Authors: Li F / Wu S / Huang S / Lv L / Cao Y / Bao H / Sun P / Bai X / Yang J / Zha J / Zhao Q / Zhang H / Li D / He J / Liu Z / Li P / Lu Z / Lei D / Li K
History
DepositionFeb 7, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69004.png

Downloads & links

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Map

FileDownload / File: emd_69004.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.)
0.97 Å/pix.
x 480 pix.
= 465.36 Å		0.97 Å/pix.
x 480 pix.
= 465.36 Å		0.97 Å/pix.
x 480 pix.
= 465.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9695 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.65
Minimum - Maximum-1.2736106 - 25.082733000000001
Average (Standard dev.)0.24602368 (±1.5875454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 465.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69004_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69004_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of FMDV O/18074 and porcine-derived neutralizing monoclon...

EntireName: Complex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-29
Components
  • Complex: Complex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-29
    • Complex: FMDV O/18074
      • Protein or peptide: VP1 of capsid protein
      • Protein or peptide: VP2 of capsid protein
      • Protein or peptide: VP3 of capsid protein
      • Protein or peptide: VP4 of capsid protein
    • Complex: porcine-derived neutralizing monoclonal antibody pO18-29
      • Protein or peptide: pO18-29 VH
      • Protein or peptide: pO18-29 VL

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Supramolecule #1: Complex of FMDV O/18074 and porcine-derived neutralizing monoclon...

SupramoleculeName: Complex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-29
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FMDV O/18074

SupramoleculeName: FMDV O/18074 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Foot-and-mouth disease virus O

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Supramolecule #3: porcine-derived neutralizing monoclonal antibody pO18-29

SupramoleculeName: porcine-derived neutralizing monoclonal antibody pO18-29
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: VP1 of capsid protein

MacromoleculeName: VP1 of capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus O
Molecular weightTheoretical: 23.686809 KDa
SequenceString: TTSAGESADP VTTTVENYGG ETQAQRRQHT DVTFILDRFV KVKPQEEINV LDLMQIPAHT LVGALLRTAT YYFSDLELAV KHEGDLTWV PNGAPEAALD NTTNPTAYHK EPLTRLALPY TAPHRVLATV YNGSNKYGDT STNNVRGDLH VLAKNAERTL P TSFNYGAI ...String:
TTSAGESADP VTTTVENYGG ETQAQRRQHT DVTFILDRFV KVKPQEEINV LDLMQIPAHT LVGALLRTAT YYFSDLELAV KHEGDLTWV PNGAPEAALD NTTNPTAYHK EPLTRLALPY TAPHRVLATV YNGSNKYGDT STNNVRGDLH VLAKNAERTL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIQPST ARHKQKIVAP VKQLL

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2 of capsid protein

MacromoleculeName: VP2 of capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus O
Molecular weightTheoretical: 24.350398 KDa
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWG TNDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSITKRELYQ LTLFPHQFIN PRTNMTAHIT V PYLGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWG TNDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSITKRELYQ LTLFPHQFIN PRTNMTAHIT V PYLGVNRY DQYKVHKPWT LVVTVVAPLT VKNEGAPQIK VYANIAPTNV YVAGELPSKE

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3 of capsid protein

MacromoleculeName: VP3 of capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus O
Molecular weightTheoretical: 23.886848 KDa
SequenceString: GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNLLPGR FTNLLDVAEA CPTFLRFDSD VPYVTTKTDS DRKLVQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMVAYAPPG MEPPTTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String:
GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNLLPGR FTNLLDVAEA CPTFLRFDSD VPYVTTKTDS DRKLVQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMVAYAPPG MEPPTTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDVAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FDLRLPVDAR AQ

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4 of capsid protein

MacromoleculeName: VP4 of capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus O
Molecular weightTheoretical: 8.862206 KDa
SequenceString:
GAGQSSPTTG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTN NTQNNDWFSK LANTAFSGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: pO18-29 VH

MacromoleculeName: pO18-29 VH / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.408091 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EDKVVESGGG LVQPGGSLRL SCVGSVWDFP NYPFTWVRQA PGKGLEWLAS IGCGVNSGAT HYADSVKGRF TISRDNSVTT ASLQMDKLR TEDTARYYCT SGRRKNVGYC YRDFVGYNPL NVWGPGVEVV VTS

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Macromolecule #6: pO18-29 VL

MacromoleculeName: pO18-29 VL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 11.560792 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QTVIQEPAMS VSPGGTVTLT CALSSGSVTS DDYPGWYQQT PGQPPRQLIY GTDNRLTGVS RRFSGVISEN KATLTISGAQ AEDEADYFC DLYKSNMKIF GGGTHLTVL

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 25588
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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