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- EMDB-55620: EV-A71 (genotype B5) empty particle in complex with 16-3-3C Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-55620
TitleEV-A71 (genotype B5) empty particle in complex with 16-3-3C Fab
Map data
Sample
  • Complex: EV-A71 empty particle/16-3-3C Fab complex
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
KeywordsHand-foot-and-mouth disease / HFMD / enterovirus 71 (EV-A71) / Human antibody / VIRUS / 16-3-3C
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Human enterovirus 71
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsZhou D / Ren J / Stuart DI
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Structural and functional mapping of protective human monoclonal antibodies against enterovirus A71.
Authors: Daming Zhou / Abhay Kotecha / James T Kelly / Peng-Nien Huang / Yi-Yin Chen / Thomas S Walter / Helen M E Duyvesteyn / Raymond J Owens / Shu-Yuan Ho / Tzou-Yien Lin / Elizabeth E Fry / ...Authors: Daming Zhou / Abhay Kotecha / James T Kelly / Peng-Nien Huang / Yi-Yin Chen / Thomas S Walter / Helen M E Duyvesteyn / Raymond J Owens / Shu-Yuan Ho / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Kuan-Ying A Huang / David I Stuart /
Abstract: EV-A71 has been responsible for recent severe HFMD outbreaks. We report structures for 12 potently neutralizing human anti-EV-A71 monoclonal antibody Fabs, alone and complexed with virus. Most ...EV-A71 has been responsible for recent severe HFMD outbreaks. We report structures for 12 potently neutralizing human anti-EV-A71 monoclonal antibody Fabs, alone and complexed with virus. Most recognize the native antigenic state with epitopes that span interfaces, together covering 85% of the capsid surface. The majority (8 of 12) bind the canyon, while the others cluster around the icosahedral two- and threefold axes. Blocking SCARB2 receptor binding likely contributes to neutralization for all, and a subset induces empty particles. A predominant gene family (IGHV4-39) does not dictate a common binding pose. Long CDR-H3 loops are frequently key to binding, especially at the canyon, suggesting that antigenicity data based on antibodies with shorter CDR3s (e.g., murine) may be misleading. This dataset reveals neutralization mechanisms for recently circulating EV-A71 genotypes, which will inform immunotherapies. We demonstrate synergy in vitro between canyon binding and both two- and threefold binding antibodies to increase neutralization potency.
History
DepositionNov 8, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55620.png

Downloads & links

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Map

FileDownload / File: emd_55620.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0070862756 - 0.024392447
Average (Standard dev.)0.00039481404 (±0.0020327887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55620_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55620_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : EV-A71 empty particle/16-3-3C Fab complex

EntireName: EV-A71 empty particle/16-3-3C Fab complex
Components
  • Complex: EV-A71 empty particle/16-3-3C Fab complex
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain

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Supramolecule #1: EV-A71 empty particle/16-3-3C Fab complex

SupramoleculeName: EV-A71 empty particle/16-3-3C Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#5, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.800232 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPRSV SGSPGQSVTI TCTGSSIDVG GYNYVSWYQQ HPGKAPKLII YDVGKRPSGV PARFSGSKSG NTASLTISGL QAEDETDYY CCSYAGSDTL VFGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPRSV SGSPGQSVTI TCTGSSIDVG GYNYVSWYQQ HPGKAPKLII YDVGKRPSGV PARFSGSKSG NTASLTISGL QAEDETDYY CCSYAGSDTL VFGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #2: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.43933 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFD DYVMHWVRQA PGKGLEWVSS ISWHGGSIAY AGSVKGRFTI SRDNARNSLF LQMNSLRTE DTALYFCAKD GPSSGWSYQN YYNAMDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFD DYVMHWVRQA PGKGLEWVSS ISWHGGSIAY AGSVKGRFTI SRDNARNSLF LQMNSLRTE DTALYFCAKD GPSSGWSYQN YYNAMDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKHHHHHH

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus 71
Molecular weightTheoretical: 27.546143 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
SequenceString: IGASSNTSDE SMIETRCVLN SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVAC TPTGQVVPQL LQYMFVPPGA PKPDSRESLA WQTATNPSVF VKLTDPPAQV SVPFMSPASA YQWFYDGYPT F GEHKQEKD ...String:
IGASSNTSDE SMIETRCVLN SHSTAETTLD SFFSRAGLVG EIDLPLEGTT NPNGYANWDI DITGYAQMRR KVELFTYMRF DAEFTFVAC TPTGQVVPQL LQYMFVPPGA PKPDSRESLA WQTATNPSVF VKLTDPPAQV SVPFMSPASA YQWFYDGYPT F GEHKQEKD LEYGACPNNM MGTFSVRTVG SSKSKYPLVV RIYMRMKHVR AWIPRPMRNQ NYLFKANPNY AGNSIKPTGT SR TAITTL

UniProtKB: Genome polyprotein

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Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human enterovirus 71
Molecular weightTheoretical: 27.814262 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
SequenceString: SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDDDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAILPE YVIGTVAGGT GTEDSHPPYK QTQPGADGFE L QHPYVLDA ...String:
SPSAEACGYS DRVAQLTIGN STITTQEAAN IIVGYGEWPS YCSDDDATAV DKPTRPDVSV NRFYTLDTKL WEKSSKGWYW KFPDVLTET GVFGQNAQFH YLYRSGFCIH VQCNASKFHQ GALLVAILPE YVIGTVAGGT GTEDSHPPYK QTQPGADGFE L QHPYVLDA GIPISQLTIC PHQWINLRTN NCATIIVPYM NTLPFDSALN HCNFGLLVVP ISPLDFDQGA TPVIPITITL AP MCSEFAG LRQAVTQ

UniProtKB: Genome polyprotein

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Macromolecule #5: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus 71
Molecular weightTheoretical: 26.558305 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
SequenceString: GFPTEPKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRDGPWQST MLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV ...String:
GFPTEPKPGT NQFLTTDDGV SAPILPNFHP TPCIHIPGEV RNLLELCQVE TILEVNNVPT NATSLMERLR FPVSAQAGKG ELCAVFRAD PGRDGPWQST MLGQLCGYYT QWSGSLEVTF MFTGSFMATG KMLIAYTPPG GPLPKDRATA MLGTHVIWDF G LQSSVTLV IPWISNTHYR AHARDGVFDY YTTGLVSFWY QTNYVVPIGA PNTAYIIALA AAQKNFTMKL CKDTSHILQT AS IQ

UniProtKB: Genome polyprotein

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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 POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3vbh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 823
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-9t6z:
EV-A71 (genotype B5) empty particle in complex with 16-3-3C Fab

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