[English] 日本語
Yorodumi
- EMDB-31556: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31556
TitleComplex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
Map data
Sample
  • Complex: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
    • Complex: FMDV A/AF/72
      • Protein or peptide: A/AF/72 VP1
      • Protein or peptide: A/AF/72 VP2
      • Protein or peptide: A/AF/72 VP3
      • Protein or peptide: Capsid protein VP0
    • Complex: and bovine neutralizing scFv antibody R55
      • Protein or peptide: IG HEAVY CHAIN VARIABLE REGION
      • Protein or peptide: IG LAMDA CHAIN VARIABLE REGION
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : ...L-peptidase / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus / Bos taurus (cattle) / Foot-and-mouth disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHe Y / Li K / Lou Z
CitationJournal: J Virol / Year: 2021
Title: Structures of Foot-and-Mouth Disease Virus with Bovine Neutralizing Antibodies Reveal the Determinant of Intraserotype Cross-Neutralization.
Authors: Yong He / Kun Li / Li Wang / Zixian Sun / Yimei Cao / Pinghua Li / Pu Sun / Huifang Bao / Shasha Zhou / Sheng Wang / Xingwen Bai / Xuerong Liu / Lixia Zhao / Xiuli Fan / Zaixin Liu / Zengjun ...Authors: Yong He / Kun Li / Li Wang / Zixian Sun / Yimei Cao / Pinghua Li / Pu Sun / Huifang Bao / Shasha Zhou / Sheng Wang / Xingwen Bai / Xuerong Liu / Lixia Zhao / Xiuli Fan / Zaixin Liu / Zengjun Lu / Cheng Yang / Zhiyong Lou /
Abstract: Foot-and-mouth disease virus (FMDV) exhibits broad antigenic diversity with poor intraserotype cross-neutralizing activity. Studies of the determinant involved in this diversity are essential for the ...Foot-and-mouth disease virus (FMDV) exhibits broad antigenic diversity with poor intraserotype cross-neutralizing activity. Studies of the determinant involved in this diversity are essential for the development of broadly protective vaccines. In this work, we isolated a bovine antibody, designated R55, that displays cross-reaction with both FMDV A/AF/72 (hereafter named FMDV-AAF) and FMDV A/WH/09 (hereafter named FMDV-AWH) but only has a neutralizing effect on FMDV-AWH. Near-atomic resolution structures of FMDV-AAF-R55 and FMDV-AWH-R55 show that R55 engages the capsids of both FMDV-AAF and FMDV-AWH near the icosahedral 3-fold axis and binds to the βB and BC/HI-loops of VP2 and to the B-B knob of VP3. The common interaction residues are highly conserved, which is the major determinant for cross-reaction with both FMDV-AAF and FMDV-AWH. In addition, the cryo-EM structure of the FMDV-AWH-R55 complex also shows that R55 binds to E70 located at the VP3 BC-loop in an adjacent pentamer, which enhances the acid and thermal stabilities of the viral capsid. This may prevent capsid dissociation and genome release into host cells, eventually leading to neutralization of the viral infection. In contrast, R55 binds only to the FMDV-AAF capsid within one pentamer due to the E70G variation, which neither enhances capsid stability nor neutralizes FMDV-AAF infection. The E70G mutation is the major determinant involved in the neutralizing differences between FMDV-AWH and FMDV-AAF. The crucial amino acid E70 is a key component of the neutralizing epitopes, which may aid in the development of broadly protective vaccines. Foot-and-mouth disease virus (FMDV) causes a highly contagious and economically devastating disease in cloven-hoofed animals, and neutralizing antibodies play critical roles in the defense against viral infections. Here, we isolated a bovine antibody (R55) using the single B cell antibody isolation technique. Enzyme-linked immunosorbent assays (ELISA) and virus neutralization tests (VNT) showed that R55 displays cross-reactions with both FMDV-AWH and FMDV-AAF but only has a neutralizing effect on FMDV-AWH. Cryo-EM structures, fluorescence-based thermal stability assays and acid stability assays showed that R55 engages the capsid of FMDV-AWH near the icosahedral 3-fold axis and informs an interpentamer epitope, which overstabilizes virions to hinder capsid dissociation to release the genome, eventually leading to neutralization of viral infection. The crucial amino acid E70 forms a key component of neutralizing epitopes, and the determination of the E70G mutation involved in the neutralizing differences between FMDV-AWH and FMDV-AAF could aid in the development of broadly protective vaccines.
History
DepositionJul 20, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7fej
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7fej
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31556.png

Downloads & links

-
Map

FileDownload / File: emd_31556.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.0032 / Movie #1: 0.023
Minimum - Maximum-0.04749602 - 0.08822531
Average (Standard dev.)0.0014863542 (±0.0058737355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-239-239-239
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z446.400446.400446.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS-239-239-239
NC/NR/NS480480480
D min/max/mean-0.0470.0880.001

-
Supplemental data

-
Sample components

-
Entire : Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55

EntireName: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
Components
  • Complex: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
    • Complex: FMDV A/AF/72
      • Protein or peptide: A/AF/72 VP1
      • Protein or peptide: A/AF/72 VP2
      • Protein or peptide: A/AF/72 VP3
      • Protein or peptide: Capsid protein VP0
    • Complex: and bovine neutralizing scFv antibody R55
      • Protein or peptide: IG HEAVY CHAIN VARIABLE REGION
      • Protein or peptide: IG LAMDA CHAIN VARIABLE REGION

-
Supramolecule #1: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55

SupramoleculeName: Complex of FMDV A/AF/72 and bovine neutralizing scFv antibody R55
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Foot-and-mouth disease virus

-
Supramolecule #2: FMDV A/AF/72

SupramoleculeName: FMDV A/AF/72 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Bos taurus (cattle)

-
Supramolecule #3: and bovine neutralizing scFv antibody R55

SupramoleculeName: and bovine neutralizing scFv antibody R55 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

-
Macromolecule #1: A/AF/72 VP1

MacromoleculeName: A/AF/72 VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.417545 KDa
SequenceString: TTTTGESADP VTTTVENYGG ETQVQRRQHT NVGFIMDRFV KIPSQSPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHDDNLTWV PNGAPETALH NTSNPTAYRK GPFTRLALPY TAPHRVLATV YNGTTKYSTG NAGRRGDLGS LAARVAAQLP A SFNFGAIR ...String:
TTTTGESADP VTTTVENYGG ETQVQRRQHT NVGFIMDRFV KIPSQSPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHDDNLTWV PNGAPETALH NTSNPTAYRK GPFTRLALPY TAPHRVLATV YNGTTKYSTG NAGRRGDLGS LAARVAAQLP A SFNFGAIR ATVIHELLVR MKRAELYCPR PLLAVEVTSQ DRHKQRIIAP AKQL

-
Macromolecule #2: A/AF/72 VP2

MacromoleculeName: A/AF/72 VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.561641 KDa
SequenceString: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFDWT TDKAFGHLEK LELPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEY KDFTLREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String:
DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFDWT TDKAFGHLEK LELPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEY KDFTLREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYKKHKPWT LVVMVLSPLT VNNSGAGQIK VYANIAPTYV HVAGELPSKE

-
Macromolecule #3: A/AF/72 VP3

MacromoleculeName: A/AF/72 VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.142053 KDa
SequenceString: GIVPVACSAG YGGLVTTDPK TADPIYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADG QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGPTDSKA RYMVAYVPPG METPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String:
GIVPVACSAG YGGLVTTDPK TADPIYGMVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTRADG QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGPTDSKA RYMVAYVPPG METPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVAET TNVQGWVCIY QITHGKAEDD TLVVSLSAGK DFELRLPIDP RSQ

-
Macromolecule #4: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 8.805154 KDa
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTN NTQNNDWFSK LASSAFTGLF GALLA

-
Macromolecule #5: IG HEAVY CHAIN VARIABLE REGION

MacromoleculeName: IG HEAVY CHAIN VARIABLE REGION / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 13.615155 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLRESGPS LVKPSQTLSL TCTVSGFSLS DYAVGWVRQA PGKALEFLGS ISTGGNTGYN PALKSRLSIT KDNSKNQVSL SLSSVTTED TATYYCTKSI HSYSVFEYTY MQYVDAWGQG LLVPVSS

-
Macromolecule #6: IG LAMDA CHAIN VARIABLE REGION

MacromoleculeName: IG LAMDA CHAIN VARIABLE REGION / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 12.88685 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
WAQAVLTQPS SVSGSLGQRV SITCSGSSNN IGRYDVGWYQ QIPGSGLRTI IYASKNRPSG VPDRFSGSRS GNTATLTISS LQAEDEADY FCATGDYSSS TSVFGSGTTL TVLGDYKDDD DKGG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25317

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more