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- EMDB-54003: EV-A71 (genotype B5) in complex with 17-2-12A Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-54003
TitleEV-A71 (genotype B5) in complex with 17-2-12A Fab
Map data
Sample
  • Complex: EV-A71/17-2-12A Fab complex
    • Complex: EV-A71
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Capsid protein
    • Complex: 17-2-12A Fab
      • Protein or peptide: light chain
      • Protein or peptide: heavy chain
  • Ligand: SPHINGOSINE
KeywordsHand-foot-and-mouth disease / HFMD / enterovirus 71 (EV-A71) / Human antibody / VIRUS / 17-2-12A
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 / virion component / viral capsid / ribonucleoside triphosphate phosphatase 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 / virion component / viral capsid / ribonucleoside triphosphate phosphatase activity / host cell / 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 / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / : / 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 superfamily / : / 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 / Capsid protein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71 / Chlorocebus aethiops (grivet monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: Science Advances / Year: 2026
Title: Structural and functional mapping of protective human monoclonal antibodies against enterovirus A71
Authors: Zhou D / Kotecha A / Kelly JT / Huang P / Chen Y / Walter TS / Duyvesteyn HME / Owens RJ / Ho S / Lin T / Fry EE / Ren J / Huang K / Stuart DI
History
DepositionJun 11, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54003.png

Downloads & links

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Map

FileDownload / File: emd_54003.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.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.2839897 - 0.39980254
Average (Standard dev.)0.0013470489 (±0.022582993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54003_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_54003_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : EV-A71/17-2-12A Fab complex

EntireName: EV-A71/17-2-12A Fab complex
Components
  • Complex: EV-A71/17-2-12A Fab complex
    • Complex: EV-A71
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Capsid protein
    • Complex: 17-2-12A Fab
      • Protein or peptide: light chain
      • Protein or peptide: heavy chain
  • Ligand: SPHINGOSINE

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Supramolecule #1: EV-A71/17-2-12A Fab complex

SupramoleculeName: EV-A71/17-2-12A Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Enterovirus A71

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Supramolecule #2: EV-A71

SupramoleculeName: EV-A71 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)

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Supramolecule #3: 17-2-12A Fab

SupramoleculeName: 17-2-12A Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
Molecular weightTheoretical: 32.748754 KDa
SequenceString: GDRVADVIES SIGDSVSRAL TQALPAPTGQ NTQVSSHRLD TGEVPALQAA EIGASSNTSD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLEG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGQVVPQ LLQYMFVPPG A PKPDSRES ...String:
GDRVADVIES SIGDSVSRAL TQALPAPTGQ NTQVSSHRLD TGEVPALQAA EIGASSNTSD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLEG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGQVVPQ LLQYMFVPPG A PKPDSRES LAWQTATNPS VFVKLTDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHKQEK DLEYGACPNN MMGTFSVRTV GS SKSKYPL VVRIYMRMKH VRAWIPRPMR NQNYLFKANP NYAGNSIKPT GTSRTAITTL

UniProtKB: Genome polyprotein

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
Molecular weightTheoretical: 27.814262 KDa
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 #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
Molecular weightTheoretical: 26.558305 KDa
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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Macromolecule #4: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
Molecular weightTheoretical: 7.501162 KDa
SequenceString:
MGSQVSTQRS GSHENSNSAT EGSTINYTTI NYYKDSYAAT AGKQSLKQDP DKFANPVKDI FTEMAAPLK

UniProtKB: Capsid protein

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Macromolecule #5: light chain

MacromoleculeName: light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.163746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAVVTQEPSL TVSPGGTVTL TCASSTGAVT SDYYPNWFQQ KPGQAPRSLI YSTSNTHSWT PARFSGSLLG GKAALTLSNV QPKDEAEYF CLLYYGGSQL WVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QAVVTQEPSL TVSPGGTVTL TCASSTGAVT SDYYPNWFQQ KPGQAPRSLI YSTSNTHSWT PARFSGSLLG GKAALTLSNV QPKDEAEYF CLLYYGGSQL WVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #6: heavy chain

MacromoleculeName: heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.209197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG LVQPGGSLRL SCAASGFTFN SYAMNWVRQA PGRGLEWVSV ISDTGGTTYY TKSVKGRFTV SRDNSKNTLY LDLNSLRAE DTAIYYCAKS VAARRFYFYY GMDAWGQGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVESGGG LVQPGGSLRL SCAASGFTFN SYAMNWVRQA PGRGLEWVSV ISDTGGTTYY TKSVKGRFTV SRDNSKNTLY LDLNSLRAE DTAIYYCAKS VAARRFYFYY GMDAWGQGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KHHHHHH

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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 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
Sample stageCooling holder cryogen: NITROGEN
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40169
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9rip:
EV-A71 (genotype B5) in complex with 17-2-12A Fab

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