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- PDB-7d3m: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -

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Basic information

Entry
Database: PDB / ID: 7d3m
TitleFOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY R50
Components
  • O/TIBET/99 VP1
  • O/TIBET/99 VP2
  • O/TIBET/99 VP3
  • O/TIBET/99 VP4
  • R50 VH
  • R50 VL
KeywordsVIRUS / FOOT AND MOUTH DISEASE VIRUS / FMDV
Biological speciesBos taurus (cattle)
Foot-and-mouth disease virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 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

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Structure visualization

Movie
  • 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: R50 VH
L: R50 VL


Theoretical massNumber of molelcules
Total (without water)111,3046
Polymers111,3046
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: R50 VH
L: R50 VL
x 60


Theoretical massNumber of molelcules
Total (without water)6,678,225360
Polymers6,678,225360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: R50 VH
L: R50 VL
x 5


  • icosahedral pentamer
  • 557 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)556,51930
Polymers556,51930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: O/TIBET/99 VP1
2: O/TIBET/99 VP2
3: O/TIBET/99 VP3
4: O/TIBET/99 VP4
H: R50 VH
L: R50 VL
x 6


  • icosahedral 23 hexamer
  • 668 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)667,82236
Polymers667,82236
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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 / 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
#5: Protein R50 VH


Mass: 18081.119 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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Antibody , 1 types, 1 molecules L

#6: Antibody R50 VL


Mass: 12705.525 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-IDSource
1Foot-and-mouth disease virus and R50 V H/LCOMPLEXall0MULTIPLE SOURCES
2Foot-and-mouth disease virusCOMPLEX#1-#41NATURAL
3R50 V H/LCOMPLEX#5-#61RECOMBINANT
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 FIELDBright-field microscopy
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
13.94FSC 0.143 CUT-OFF1546017D3MPOINT
23.94FSC 0.143 CUT-OFF1546027D3MPOINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 3.94 Å

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