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- PDB-7d3k: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -

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Entry
Database: PDB / ID: 7d3k
TitleFOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY B77
Components
  • B77 VH
  • B77 VL
  • O/TIBET/99 VP1
  • O/TIBET/99 VP2
  • O/TIBET/99 VP3
  • O/TIBET/99 VP4
KeywordsVIRUS / FOOT AND MOUTH DISEASE VIRUS / FMDV
Biological speciesBos taurus (cattle)
Foot-and-mouth disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHe, Y. / Lou, Z.
CitationJournal: PLoS Pathog / Year: 2021
Title: Structures of Foot-and-mouth Disease Virus with neutralizing antibodies derived from recovered natural host reveal a mechanism for cross-serotype neutralization.
Authors: Yong He / Kun Li / Yimei Cao / Zixian Sun / Pinghua Li / Huifang Bao / Sheng Wang / Guoqiang Zhu / Xingwen Bai / Pu Sun / Xuerong Liu / Cheng Yang / Zaixin Liu / Zengjun Lu / Zihe Rao / Zhiyong Lou /
Abstract: The development of a universal vaccine against foot-and-mouth disease virus (FMDV) is hindered by cross-serotype antigenic diversity and by a lack of knowledge regarding neutralization of the virus ...The development of a universal vaccine against foot-and-mouth disease virus (FMDV) is hindered by cross-serotype antigenic diversity and by a lack of knowledge regarding neutralization of the virus in natural hosts. In this study, we isolated serotype O-specific neutralizing antibodies (NAbs) (F145 and B77) from recovered natural bovine hosts by using the single B cell antibody isolation technique. We also identified a serotype O/A cross-reacting NAb (R50) and determined virus-NAb complex structures by cryo-electron microscopy at near-atomic resolution. F145 and B77 were shown to engage the capsid of FMDV-O near the icosahedral threefold axis, binding to the BC/HI-loop of VP2. In contrast, R50 engages the capsids of both FMDV-O and FMDV-A between the 2- and 5-fold axes and binds to the BC/EF/GH-loop of VP1 and to the GH-loop of VP3 from two adjacent protomers, revealing a previously unknown antigenic site. The cross-serotype neutralizing epitope recognized by R50 is highly conserved among serotype O/A. These findings help to elucidate FMDV neutralization by natural hosts and provide epitope information for the development of a universal vaccine for cross-serotype protection against FMDV.
History
DepositionSep 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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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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: B77 VH
L: B77 VL


Theoretical massNumber of molelcules
Total (without water)106,7916
Polymers106,7916
Non-polymers00
Water00
1
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: B77 VH
L: B77 VL
x 60


Theoretical massNumber of molelcules
Total (without water)6,407,465360
Polymers6,407,465360
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: B77 VH
L: B77 VL
x 5


  • icosahedral pentamer
  • 534 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)533,95530
Polymers533,95530
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: B77 VH
L: B77 VL
x 6


  • icosahedral 23 hexamer
  • 641 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)640,74636
Polymers640,74636
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 , 4 types, 4 molecules 1234

#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 / Mutation: YES / 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

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Antibody , 2 types, 2 molecules HL

#5: Antibody B77 VH


Mass: 13325.990 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
#6: Antibody B77 VL


Mass: 12947.993 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

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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-IDSourceDetails
1Foot-and-mouth disease virusCOMPLEXall0MULTIPLE SOURCES
2Foot-and-mouth disease virusCOMPLEX#1-#41NATURAL
3B77 V H/LCOMPLEX#5-#61RECOMBINANTSingle-chain fragment variable (scFv) was designed by splicing the VH and VL genes using a flexible linker (GGGGSGGGGSGGGGS).The C-termini of the scFv included a His tag.
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Foot-and-mouth disease virus12110
33Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Cricetinae gen. sp.
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 TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.63 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.9FSC 0.143 CUT-OFF1546017D3KPOINT
23.9FSC 0.143 CUT-OFF1546027D3KPOINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 3.9 Å

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