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- PDB-7eo0: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -

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Basic information

Entry
Database: PDB / ID: 7eo0
TitleFOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY C4
Components
  • Ig heavy chain variable region
  • Ig lamda chain variable region
  • O/TIBET/99 VP1
  • O/TIBET/99 VP2
  • O/TIBET/99 VP3
  • O/TIBET/99 VP4
KeywordsVIRUS / FOOT AND MOUTH DISEASE VIRUS / FMDV
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig lamda chain variable region / Ig heavy chain variable region
Similarity search - Component
Biological speciesBos taurus (cattle)
Foot-and-mouth disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsHe, Y. / Li, K.
CitationJournal: J Virol / Year: 2021
Title: Two Cross-Protective Antigen Sites on Foot-and-Mouth Disease Virus Serotype O Structurally Revealed by Broadly Neutralizing Antibodies from Cattle.
Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Sheng Wang / Pu Sun / Huifang Bao / Yimei Cao / Xuerong Liu / Guoqiang Zhu / Yali Song / Xingwen Bai / Xueqing Ma / Yuanfang Fu / Hong Yuan / Jing ...Authors: Kun Li / Yong He / Li Wang / Pinghua Li / Sheng Wang / Pu Sun / Huifang Bao / Yimei Cao / Xuerong Liu / Guoqiang Zhu / Yali Song / Xingwen Bai / Xueqing Ma / Yuanfang Fu / Hong Yuan / Jing Zhang / Jian Wang / Yingli Chen / Dong Li / Zhiyong Lou / Zaixin Liu / Zengjun Lu /
Abstract: Foot-and-mouth disease virus (FMDV) is a highly contagious virus that infects cloven-hoofed animals. Neutralizing antibodies play critical roles in antiviral infection. Although five known antigen ...Foot-and-mouth disease virus (FMDV) is a highly contagious virus that infects cloven-hoofed animals. Neutralizing antibodies play critical roles in antiviral infection. Although five known antigen sites that induce neutralizing antibodies have been defined, studies on cross-protective antigen sites are still scarce. We mapped two cross-protective antigen sites using 13 bovine-derived broadly neutralizing monoclonal antibodies (bnAbs) capable of neutralizing 4 lineages within 3 topotypes of FMDV serotype O. One antigen site was formed by a novel cluster of VP3-focused epitopes recognized by bnAb C4 and C4-like antibodies. The cryo-electron microscopy (cryo-EM) structure of the FMDV-OTi (O/Tibet/99)-C4 complex showed close contact with VP3 and a novel interprotomer antigen epitope around the icosahedral 3-fold axis of the FMDV particle, which is far beyond the known antigen site 4. The key determinants of the neutralizing function of C4 and C4-like antibodies on the capsid were βB (T65), the B-C loop (T68), the E-F loop (E131 and K134), and the H-I loop (G196), revealing a novel antigen site on VP3. The other antigen site comprised two group epitopes on VP2 recognized by 9 bnAbs (B57, B73, B77, B82, F28, F145, F150, E46, and E54), which belong to the known antigen site 2 of FMDV serotype O. Notably, bnAb C4 potently promoted FMDV RNA release in response to damage to viral particles, suggesting that the targeted epitope contains a trigger mechanism for particle disassembly. This study revealed two cross-protective antigen sites that can elicit cross-reactive neutralizing antibodies in cattle and provided new structural information for the design of a broad-spectrum molecular vaccine against FMDV serotype O. FMDV is the causative agent of foot-and-mouth disease (FMD), which is one of the most contagious and economically devastating diseases of domestic animals. The antigenic structure of FMDV serotype O is rather complicated, especially for those sites that can elicit a cross-protective neutralizing antibody response. Monoclonal neutralization antibodies provide both crucial defense components against FMDV infection and valuable tools for fine analysis of the antigenic structure. In this study, we found a cluster of novel VP3-focused epitopes using 13 bnAbs against FMDV serotype O from natural host cattle, which revealed two cross-protective antigen sites on VP2 and VP3. Antibody C4 targeting this novel epitope potently promoted viral particle disassembly and RNA release before infection, which may indicate a vulnerable region of FMDV. This study reveals new structural information about cross-protective antigen sites of FMDV serotype O, providing valuable and strong support for future research on broad-spectrum vaccines against FMD.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.3Feb 23, 2022Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: Ig heavy chain variable region
L: Ig lamda chain variable region


Theoretical massNumber of molelcules
Total (without water)107,2276
Polymers107,2276
Non-polymers00
Water0
1
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: Ig heavy chain variable region
L: Ig lamda chain variable region
x 60


Theoretical massNumber of molelcules
Total (without water)6,433,591360
Polymers6,433,591360
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
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: Ig heavy chain variable region
L: Ig lamda chain variable region
x 5


  • icosahedral pentamer
  • 536 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)536,13330
Polymers536,13330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: Ig heavy chain variable region
L: Ig lamda chain variable region
x 6


  • icosahedral 23 hexamer
  • 643 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)643,35936
Polymers643,35936
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

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Protein , 5 types, 5 molecules 1234H

#1: Protein O/TIBET/99 VP1


Mass: 23524.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#2: Protein O/TIBET/99 VP2


Mass: 24338.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#3: Protein O/TIBET/99 VP3


Mass: 23875.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#4: Protein O/TIBET/99 VP4


Mass: 8778.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus
#5: Protein Ig heavy chain variable region


Mass: 13914.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A6B9SE04

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Antibody , 1 types, 1 molecules L

#6: Antibody Ig lamda chain variable region


Mass: 12794.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A6B9SCH7

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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
1FMDV-OTi-C4COMPLEXall0MULTIPLE SOURCES
2FOOT AND MOUTH DISEASE VIRUS O/TIBET/99COMPLEX#1-#41NATURAL
3C4 scFvCOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Foot-and-mouth disease virus12110
23Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Buffer solutionpH: 7.4
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: OTHER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14458 / Symmetry type: POINT
RefinementHighest resolution: 3.75 Å

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