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- EMDB-54004: EV-A71 (genotype C4) in complex with 16-2-11B Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-54004
TitleEV-A71 (genotype C4) in complex with 16-2-11B Fab
Map data
Sample
  • Complex: EV-A71/16-2-11B Fab complex
    • Complex: EV-A71
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: VP4
    • Complex: 16-2-11B 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 / 16-2-11B
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 / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / Genome polyprotein / VP4
Similarity search - Component
Biological speciesEnterovirus A71 / Chlorocebus aethiops (grivet monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_54004.png

Downloads & links

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Map

FileDownload / File: emd_54004.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.)
1.39 Å/pix.
x 400 pix.
= 556. Å		1.39 Å/pix.
x 400 pix.
= 556. Å		1.39 Å/pix.
x 400 pix.
= 556. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.1623963 - 0.2736564
Average (Standard dev.)0.0012405802 (±0.017096912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 556.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54004_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EV-A71/16-2-11B Fab complex

EntireName: EV-A71/16-2-11B Fab complex
Components
  • Complex: EV-A71/16-2-11B Fab complex
    • Complex: EV-A71
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: VP4
    • Complex: 16-2-11B Fab
      • Protein or peptide: light chain
      • Protein or peptide: heavy chain
  • Ligand: SPHINGOSINE

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Supramolecule #1: EV-A71/16-2-11B Fab complex

SupramoleculeName: EV-A71/16-2-11B 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: 16-2-11B Fab

SupramoleculeName: 16-2-11B 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: 32.727891 KDa
SequenceString: GDRVADVIES SIGDSVSRAL THALPAPTGQ NTQVSSHRLD TGKVPALQAA EIGASSNASD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLKG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGEVVPQ LLQYMFVPPG A PKPDSRES ...String:
GDRVADVIES SIGDSVSRAL THALPAPTGQ NTQVSSHRLD TGKVPALQAA EIGASSNASD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLKG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGEVVPQ LLQYMFVPPG A PKPDSRES LAWQTATNPS VFVKLSDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHKQEK DLEYGAMPNN MMGTFSVRTV GT SKSKYPL VVRIYMRMKH VRAWIPRPMR NQNYLFKANP NYAGNSIKPT GASRTAITTL

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: 26.874252 KDa
SequenceString: SDRVAQLTIG NSTITTQEAA NIIVGYGEWP SYCSDSDATA VDKPTRPDVS VNRFYTLDTK LWEKSSKGWY WKFPDVLTET GVFGQNAQF HYLYRSGFCI HVQCNASKFH QGALLVAVLP EYVIGTVAGG TGTEDTHPPY KQTQPGADGF ELQHPYVLDA G IPISQLTV ...String:
SDRVAQLTIG NSTITTQEAA NIIVGYGEWP SYCSDSDATA VDKPTRPDVS VNRFYTLDTK LWEKSSKGWY WKFPDVLTET GVFGQNAQF HYLYRSGFCI HVQCNASKFH QGALLVAVLP EYVIGTVAGG TGTEDTHPPY KQTQPGADGF ELQHPYVLDA G IPISQLTV CPHQWINLRT NNCATIIVPY INALPFDSAL NHCNFGLLVV PISPLDYDQG ATPVIPITIT LAPMCSEFAG LR QAVTQ

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 / EC number: picornain 2A
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
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 #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlorocebus aethiops (grivet monkey)
Molecular weightTheoretical: 6.380943 KDa
SequenceString:
SHENSNSATE GSTINYTTIN YYKDSYAATA GKQSLKQDPD KFANPVKDIF TEMAAPLK

UniProtKB: VP4

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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: 22.870238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPASV SGSPGQSITI SCIGTSSDID AYNYVSWYQQ HPGKAPKVII YDVRNRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CSAFTTSSTL VFGGGTKLAV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPASV SGSPGQSITI SCIGTSSDID AYNYVSWYQQ HPGKAPKVII YDVRNRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CSAFTTSSTL VFGGGTKLAV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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: 25.295326 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKTSGYTFT NFYMHWVRQA PGQGLEWMGV MDPRGGGTVY AQRFQGRLTV TRDTSTSTVY MDLSSLKSE DTAVYYCARN YNGYCAGDCY SPDFWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGASVKV SCKTSGYTFT NFYMHWVRQA PGQGLEWMGV MDPRGGGTVY AQRFQGRLTV TRDTSTSTVY MDLSSLKSE DTAVYYCARN YNGYCAGDCY SPDFWGQGTL 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: 27.0 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5881
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-9riq:
EV-A71 (genotype C4) in complex with 16-2-11B Fab

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