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- PDB-8hbi: FMDV (A/TUR/14/98) in complex with M688F -

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Basic information

Entry
Database: PDB / ID: 8hbi
TitleFMDV (A/TUR/14/98) in complex with M688F
Components
  • M688F nab
  • VP1 of capsid protein
  • VP2 of capsid protein
  • VP3 of capsid protein
  • VP4 of capsid protein
KeywordsVIRUS / FMDV / antibody
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus coat protein / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Foot-and-mouth disease virus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi, H.Z. / Dong, H. / Liu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Foot-and-mouth disease virus antigenic landscape and reduced immunogenicity elucidated in atomic detail.
Authors: Haozhou Li / Pan Liu / Hu Dong / Aldo Dekker / Michiel M Harmsen / Huichen Guo / Xiangxi Wang / Shiqi Sun /
Abstract: Unlike most other picornaviruses, foot-and-mouth disease (FMD) intact virions (146S) dissociate easily into small pentameric subunits (12S). This causes a dramatically decreased immunogenicity by a ...Unlike most other picornaviruses, foot-and-mouth disease (FMD) intact virions (146S) dissociate easily into small pentameric subunits (12S). This causes a dramatically decreased immunogenicity by a mechanism that remains elusive. Here, we present the high-resolution structures of 12S (3.2 Å) and its immune complex of a single-domain antibody (VHH) targeting the particle interior (3.2 Å), as well as two 146S-specific VHHs complexed to distinct sites on the 146S capsid surface (3.6 Å and 2.9 Å). The antigenic landscape of 146S is depicted using 13 known FMD virus-antibody complexes. Comparison of the immunogenicity of 146S and 12S in pigs, focusing on the resulting antigenic sites and incorporating structural analysis, reveals that dissociation of 146S leads to structural alteration and destruction of multiple epitopes, resulting in significant differences in antibody profiles/lineages induced by 12S and 146S. Furthermore, 146S generates higher synergistic neutralizing antibody titers compared to 12S, whereas both particles induce similar total FMD virus specific antibody titers. This study can guide the structure-based rational design of novel multivalent and broad-spectrum recombinant vaccines for protection against FMD.
History
DepositionOct 28, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein


Theoretical massNumber of molelcules
Total (without water)94,6115
Polymers94,6115
Non-polymers00
Water00
1
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,676,634300
Polymers5,676,634300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 5


  • icosahedral pentamer
  • 473 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)473,05325
Polymers473,05325
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
E: M688F nab
A: VP1 of capsid protein
B: VP2 of capsid protein
C: VP3 of capsid protein
D: VP4 of capsid protein
x 6


  • icosahedral 23 hexamer
  • 568 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)567,66330
Polymers567,66330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Antibody M688F nab


Mass: 13861.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Yeast centromeric expression vector p416GPD (others)
#2: Protein VP1 of capsid protein


Mass: 23111.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#3: Protein VP2 of capsid protein


Mass: 24575.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#4: Protein VP3 of capsid protein


Mass: 24284.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
#5: Protein VP4 of capsid protein


Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus A / References: UniProt: A0A7D5BJ70
Has protein modificationN

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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

ComponentName: FMDV capsid protein in complex with M688F nab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Foot-and-mouth disease virus A
Buffer solutionpH: 7
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25824 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076317
ELECTRON MICROSCOPYf_angle_d0.6418604
ELECTRON MICROSCOPYf_dihedral_angle_d16.346866
ELECTRON MICROSCOPYf_chiral_restr0.047954
ELECTRON MICROSCOPYf_plane_restr0.0051114

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