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- PDB-9wph: Complex of FMDV O/18074 and porcine-derived neutralizing monoclon... -

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Basic information

Entry
Database: PDB / ID: 9wph
TitleComplex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-10
Components
  • VP1 of capsid protein
  • VP2 of capsid protein
  • VP3 of capsid protein
  • VP4 of capsid protein
  • pO18-10 VH
  • pO18-10 VL
KeywordsVIRUS / Foot-and-mouth disease virus O / Sus scrofa / VIRUS/IMMUNE SYSTEM / 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 speciesSus scrofa (pig)
Foot-and-mouth disease virus O
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsWu, S. / Zhu, Z. / Lei, D.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171300 China
Other governmentR2405
Other government2021YFD1800300
National Natural Science Foundation of China (NSFC)32373028 China
Other governmentCAAS-CSLPDCP-202402
CitationJournal: To Be Published
Title: Structural basis of a conserved, broad antigen region surrounding the five-fold axis of foot-and-mouth disease virus revealed by swine neutralizing antibodies
Authors: Zhao, Q. / Wu, S. / Li, F. / Huang, S. / Yang, J. / Sun, Y. / Li, P. / Cao, Y. / Bao, H. / Sun, P. / Bai, X. / Zhao, Z. / Zhang, J. / Yuan, H. / Fu, Y. / Ma, X. / Li, D. / Zhang, Q. / Qian, ...Authors: Zhao, Q. / Wu, S. / Li, F. / Huang, S. / Yang, J. / Sun, Y. / Li, P. / Cao, Y. / Bao, H. / Sun, P. / Bai, X. / Zhao, Z. / Zhang, J. / Yuan, H. / Fu, Y. / Ma, X. / Li, D. / Zhang, Q. / Qian, P. / Zhu, Z. / Li, X. / Lu, Z. / Lei, D. / Li, K.
History
DepositionSep 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: VP1 of capsid protein
2: VP2 of capsid protein
3: VP3 of capsid protein
4: VP4 of capsid protein
H: pO18-10 VH
L: pO18-10 VL


Theoretical massNumber of molelcules
Total (without water)106,2756
Polymers106,2756
Non-polymers00
Water00
1
1: VP1 of capsid protein
2: VP2 of capsid protein
3: VP3 of capsid protein
4: VP4 of capsid protein
H: pO18-10 VH
L: pO18-10 VL
x 60


Theoretical massNumber of molelcules
Total (without water)6,376,528360
Polymers6,376,528360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

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Protein , 4 types, 4 molecules 1234

#1: Protein VP1 of capsid protein


Mass: 23686.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus O / References: UniProt: A0A1P8DYS7
#2: Protein VP2 of capsid protein


Mass: 24350.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus O / References: UniProt: J9PGT1
#3: Protein VP3 of capsid protein


Mass: 23886.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus O / References: UniProt: A0A1C6ZW66
#4: Protein VP4 of capsid protein


Mass: 8862.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus O / References: UniProt: J9PGT1

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Antibody , 2 types, 2 molecules HL

#5: Antibody pO18-10 VH


Mass: 14042.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Homo sapiens (human)
#6: Antibody pO18-10 VL


Mass: 11446.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Homo sapiens (human)

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of FMDV O/18074 and porcine-derived neutralizing monoclonal antibody pO18-10COMPLEXall0MULTIPLE SOURCES
2FMDV O/18074COMPLEX#1-#41NATURAL
3porcine-derived neutralizing monoclonal antibody pO18-10COMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Foot-and-mouth disease virus O12118
33Sus scrofa (pig)9823
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
4CTFFIND4CTF correction
9cryoSPARC4.2initial Euler assignment
10cryoSPARC4.2final Euler assignment
12cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29102 / Symmetry type: POINT
RefinementHighest resolution: 2.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047060
ELECTRON MICROSCOPYf_angle_d0.5919632
ELECTRON MICROSCOPYf_dihedral_angle_d5.42972
ELECTRON MICROSCOPYf_chiral_restr0.0441086
ELECTRON MICROSCOPYf_plane_restr0.0051246

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