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- EMDB-30560: FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FR... -

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Basic information

Entry
Database: EMDB / ID: EMD-30560
TitleFOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY R50
Map data
Sample
  • Complex: Foot-and-mouth disease virus and R50 V H/L
    • Complex: Foot-and-mouth disease virus
      • Protein or peptide: O/TIBET/99 VP1
      • Protein or peptide: O/TIBET/99 VP2
      • Protein or peptide: O/TIBET/99 VP3
      • Protein or peptide: O/TIBET/99 VP4
    • Complex: R50 V H/L
      • Protein or peptide: R50 VH
      • Protein or peptide: R50 VL
KeywordsFOOT AND MOUTH DISEASE VIRUS / FMDV / VIRUS
Biological speciesFoot-and-mouth disease virus / Bos taurus (domestic cattle)
Methodsingle 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, 2020-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0032
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d3m
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7d3m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30560.png

Downloads & links

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Map

FileDownload / File: emd_30560.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 460 pix.
= 427.8 Å		0.93 Å/pix.
x 460 pix.
= 427.8 Å		0.93 Å/pix.
x 460 pix.
= 427.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0032 / Movie #1: 0.0032
Minimum - Maximum-0.089817286 - 0.13982423
Average (Standard dev.)0.0015041699 (±0.009005833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-230-230-230
Dimensions460460460
Spacing460460460
CellA=B=C: 427.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z427.800427.800427.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-230-230-230
NC/NR/NS460460460
D min/max/mean-0.0900.1400.002

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Supplemental data

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Sample components

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Entire : Foot-and-mouth disease virus and R50 V H/L

EntireName: Foot-and-mouth disease virus and R50 V H/L
Components
  • Complex: Foot-and-mouth disease virus and R50 V H/L
    • Complex: Foot-and-mouth disease virus
      • Protein or peptide: O/TIBET/99 VP1
      • Protein or peptide: O/TIBET/99 VP2
      • Protein or peptide: O/TIBET/99 VP3
      • Protein or peptide: O/TIBET/99 VP4
    • Complex: R50 V H/L
      • Protein or peptide: R50 VH
      • Protein or peptide: R50 VL

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Supramolecule #1: Foot-and-mouth disease virus and R50 V H/L

SupramoleculeName: Foot-and-mouth disease virus and R50 V H/L / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Foot-and-mouth disease virus

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Supramolecule #3: R50 V H/L

SupramoleculeName: R50 V H/L / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: O/TIBET/99 VP1

MacromoleculeName: O/TIBET/99 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.524781 KDa
SequenceString: TTSTGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNCKYGES PVTNARGDLQ VLAQKAARAL P TSFNYGAI ...String:
TTSTGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGNCKYGES PVTNARGDLQ VLAQKAARAL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPSE ARHKQKIVAP VKQLL

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Macromolecule #2: O/TIBET/99 VP2

MacromoleculeName: O/TIBET/99 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.338387 KDa
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDPFGRCYQ LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIDKRGLYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDPFGRCYQ LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIDKRGLYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNTEGAPQIK VYANIAPTNV HVAGEFPSKE

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Macromolecule #3: O/TIBET/99 VP3

MacromoleculeName: O/TIBET/99 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.875801 KDa
SequenceString: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String:
GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDAAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ

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Macromolecule #4: O/TIBET/99 VP4

MacromoleculeName: O/TIBET/99 VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 8.778129 KDa
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA

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Macromolecule #5: R50 VH

MacromoleculeName: R50 VH / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 18.081119 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLRESGPS LVKPSQTLSL TCTASGLSLS DKAVGWVRRA PTKALEWLGS IDTGSSTGYN PGLKSRLSIT KDNSRNQVSL TITSVTTED SATYYCATVH QHTSEKRTCP RAYRPDCAAR WDCPGGADCG YCNFGAGSYG RCTPFTLTYT FENYVHTWGQ G LLVTVSS

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Macromolecule #6: R50 VL

MacromoleculeName: R50 VL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 12.705525 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
WAQAVLTQPS SVSGSLGQRV SITCSGSSSN VGNGYVSWYQ LIPGSAPRTL IYGDTNRASG VPDRFSGSRA GNTATLSISS LQAEDEAEY FCASPEDSSS NANFGSGTTL TVLGDYKDDD DKGG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.63 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15460
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Image processing #2

Image processing ID2
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15460
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7d3m:
FOOT AND MOUTH DISEASE VIRUS O/TIBET/99-BOUND THE SINGLE CHAIN FRAGMEN ANTIBODY R50

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