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- EMDB-63694: Cryo-EM structure of enterovirus A71 mature virion in complex wit... -

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Entry
Database: EMDB / ID: EMD-63694
TitleCryo-EM structure of enterovirus A71 mature virion in complex with Fab CT11F9
Map data
Sample
  • Complex: Enterovirus A71 mature virion in complex with Fab CT11F9
    • Complex: Enterovirus A71 mature virion
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
    • Complex: Fab CT11F9
      • Protein or peptide: The light chain of Fab CT11F9
      • Protein or peptide: The heavy chain of Fab CT11F9
  • Ligand: SPHINGOSINE
KeywordsVIRUS / ENTEROVIRUS A71
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / DNA replication / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesEnterovirus A71 / Mus (mice) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsJiang Y / Zhu R / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Vaccines (Basel) / Year: 2025
Title: Development of In Vitro Potency Methods to Replace In Vivo Tests for Enterovirus 71 Inactivated Vaccine (Human Diploid Cell-Based/Vero Cell-Based).
Authors: Xuanxuan Zhang / Li Yi / Dan Yu / Jun Li / Xintian Li / Xing Wu / Fan Gao / Qian He / Wenhui Wang / Kaiwen Wang / Zejun Wang / Zhengling Liu / Yadong Li / Yong Zhao / Huiyi Li / Xiao Ma / ...Authors: Xuanxuan Zhang / Li Yi / Dan Yu / Jun Li / Xintian Li / Xing Wu / Fan Gao / Qian He / Wenhui Wang / Kaiwen Wang / Zejun Wang / Zhengling Liu / Yadong Li / Yong Zhao / Huiyi Li / Xiao Ma / Qingbing Zheng / Longfa Xu / Tong Cheng / Rui Zhu / Jing Guo / Jing Li / Qunying Mao / Zhenglun Liang /
Abstract: BACKGROUND: The three commercial Enterovirus 71 (EV71) inactivated vaccines which have effectively controlled the EV71 pandemic currently rely on inherent variable in vivo potency methods for batch ...BACKGROUND: The three commercial Enterovirus 71 (EV71) inactivated vaccines which have effectively controlled the EV71 pandemic currently rely on inherent variable in vivo potency methods for batch release. To align with 3R (Replacement, Reduction, Refinement) principles and enhance quality control, this study referred to WHO guidelines and the European Pharmacopoeia to develop in vitro relative potency (IVRP) methods.
METHODS: Working standards tracing to phase 3 clinical vaccines were established. Manufacture-specific IVRP methods were developed and validated per ICH Q14/Q2(R2), utilizing conformational epitope- ...METHODS: Working standards tracing to phase 3 clinical vaccines were established. Manufacture-specific IVRP methods were developed and validated per ICH Q14/Q2(R2), utilizing conformational epitope-targeting neutralizing monoclonal antibodies (MAbs). One of the MAbs (CT11F9) recognition sites was clarified with Cryo-EM. Subsequently, the performance of IVRP was assessed using varied concentrations and heat-treated vaccines. The correlation between IVRP and in vivo methods was analyzed, followed by setting IVRP specifications.
RESULTS: The manufacturer-specific working standard exhibited ED50 values comparable to those of related phase 3 clinical vaccines. All IVRP methods achieved a relative bias/precision/total error ≤ ...RESULTS: The manufacturer-specific working standard exhibited ED50 values comparable to those of related phase 3 clinical vaccines. All IVRP methods achieved a relative bias/precision/total error ≤ 15%. The IVRP methods correlated with in vivo methods ( < 0.05, r > 0.9) can discriminate EV71 antigen concentrations ( < 0.01, r > 0.99) and indicate the stability of the vaccines. Cryo-EM was adopted to identify the epitopes recognized by CT11F9, revealing that this neutralizing antibody recognizes a conformational epitope spanning VP1-3 of the same protomer. Using 31-47 batches of commercial vaccines, IVRP specifications were proposed as 0.56-1.35, 0.58-1.40, and 0.54-1.50.
CONCLUSIONS: Based on conformational epitope-targeting neutralizing MAbs, manufacturer-specific IVRP methods, which were sensitive to process variations and correlated with in vivo results, have been ...CONCLUSIONS: Based on conformational epitope-targeting neutralizing MAbs, manufacturer-specific IVRP methods, which were sensitive to process variations and correlated with in vivo results, have been established. IVRP methods provide a reliable, animal-free alternative for EV71 vaccine batch release.
History
DepositionMar 11, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63694.png

Downloads & links

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Map

FileDownload / File: emd_63694.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 576 pix.
= 576. Å		1 Å/pix.
x 576 pix.
= 576. Å		1 Å/pix.
x 576 pix.
= 576. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4406388 - 2.4703653
Average (Standard dev.)0.0012116388 (±0.123518124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 576.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63694_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_63694_half_map_2.map
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Sample components

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Entire : Enterovirus A71 mature virion in complex with Fab CT11F9

EntireName: Enterovirus A71 mature virion in complex with Fab CT11F9
Components
  • Complex: Enterovirus A71 mature virion in complex with Fab CT11F9
    • Complex: Enterovirus A71 mature virion
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
    • Complex: Fab CT11F9
      • Protein or peptide: The light chain of Fab CT11F9
      • Protein or peptide: The heavy chain of Fab CT11F9
  • Ligand: SPHINGOSINE

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Supramolecule #1: Enterovirus A71 mature virion in complex with Fab CT11F9

SupramoleculeName: Enterovirus A71 mature virion in complex with Fab CT11F9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Enterovirus A71 mature virion

SupramoleculeName: Enterovirus A71 mature virion / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Enterovirus A71

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Supramolecule #3: Fab CT11F9

SupramoleculeName: Fab CT11F9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus (mice)

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Macromolecule #1: The light chain of Fab CT11F9

MacromoleculeName: The light chain of Fab CT11F9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.474827 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIVLTQSPAI MSASPGEKVT ISCSASSSVR YMYWYQQKPG SAPKPWIYRT SNLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ YHSYPLTFGA GTKLELK

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Macromolecule #2: The heavy chain of Fab CT11F9

MacromoleculeName: The heavy chain of Fab CT11F9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.493756 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SGYYWNWIRQ FPGNKLEWMG YINYGGSNFY NPSLKNRISI TRDTSRNQFF LKLNSVTTE DTATYYCARG GYYDYDGDYW GQGTTLTVSS

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Macromolecule #3: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 32.730848 KDa
SequenceString: GDRVADVIES SIGDSVSRAL THALPAPTGQ DTQVSSHRLD TGKVPALQAA EIGASSNASD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLKG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGEVVPQ LLQYMFVPPG A PKPDSRES ...String:
GDRVADVIES SIGDSVSRAL THALPAPTGQ DTQVSSHRLD TGKVPALQAA EIGASSNASD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLKG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGEVVPQ LLQYMFVPPG A PKPDSRES LAWQTATNPS VFVKLSDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHKQEK DLEYGACPNN MMGTFSVRTV GT SKSKYPL VVRIYMRMKH VRAWIPRPMR NQNYLFKANP NYAGNSIKPT GTSRTAITTL

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 27.726135 KDa
SequenceString: SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDSDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAVLPE YVIGTVAGGT GTEDSHPPYK QTQPGADGFE L QHPYVLDA ...String:
SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDSDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAVLPE YVIGTVAGGT GTEDSHPPYK QTQPGADGFE L QHPYVLDA GIPISQLTVC PHQWINLRTN NCATIIVPYI NALPFDSALN HCNFGLLVVP ISPLDYDQGA TPVIPITITL AP MCSEFAG LRQAVTQ

UniProtKB: Genome polyprotein

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Macromolecule #5: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 26.468225 KDa
SequenceString: GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRNGPWQST LLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV ...String:
GFPTELKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRNGPWQST LLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV IPWISNTHYR AHARDGVFDY YTTGLVSIWY QTNYVVPIGA PNTAYIIALA AAQKNFTMKL CKDASDILQT GT IQ

UniProtKB: Genome polyprotein

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Macromolecule #6: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus A71
Molecular weightTheoretical: 7.501162 KDa
SequenceString:
MGSQVSTQRS GSHENSNSAT EGSTINYTTI NYYKDSYAAT AGKQSLKQDP DKFANPVKDI FTEMAAPLK

UniProtKB: Genome polyprotein

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Macromolecule #7: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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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 F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71798
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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