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- EMDB-6963: Fit R10 Fab coordinates into the cryo-EM of EV71 in complex with D6 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6963 | |||||||||
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Title | Fit R10 Fab coordinates into the cryo-EM of EV71 in complex with D6 | |||||||||
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Function / homology | ![]() 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
![]() | Wang X / Zhu L / Wang N | |||||||||
![]() | ![]() Title: Neutralization Mechanisms of Two Highly Potent Antibodies against Human Enterovirus 71. Authors: Ling Zhu / Kangwei Xu / Nan Wang / Lei Cao / Junlan Wu / Qiang Gao / Elizabeth E Fry / David I Stuart / Zihe Rao / Junzhi Wang / Xiangxi Wang / ![]() ![]() Abstract: Despite significant advances in health care, outbreaks of infections by enteroviruses (EVs) continue to plague the Asia-Pacific region every year. Enterovirus 71 (EV71) causes hand-foot-and-mouth ...Despite significant advances in health care, outbreaks of infections by enteroviruses (EVs) continue to plague the Asia-Pacific region every year. Enterovirus 71 (EV71) causes hand-foot-and-mouth disease (HFMD), for which there are currently no therapeutics. Here, we report two new antibodies, A9 and D6, that potently neutralize EV71. A9 exhibited a 50% neutralizing concentration (neut) value of 0.1 nM against EV71, which was 10-fold lower than that observed for D6. Investigation into the mechanisms of neutralization revealed that binding of A9 to EV71 blocks receptor binding but also destabilizes and damages the virus capsid structure. In contrast, D6 destabilizes the capsid only slightly but interferes more potently with the attachment of the virus to the host cells. Cryo-electron microscopy (cryo-EM) structures of A9 and D6 bound with EV71 shed light on the locations and nature of the epitopes recognized by the two antibodies. Although some regions of the epitopes recognized by the two antibodies overlap, there are differences that give rise to dissimilarities in potency as well as in the mechanisms of neutralization. Interestingly, the overlapping regions of the epitopes encompass the site that the virus uses to bind SCARB2, explaining the reason for the observed blocking of the virus-receptor interaction by the two antibodies. We also identified structural elements that might play roles in modulating the stability of the EV71 particles, including particle integrity. The molecular features of the A9 and D6 epitopes unveiled in this study open up new avenues for rationally designing antiviral drugs. During the course of viral infections, the human body produces neutralizing antibodies which play a defining role in clearing the virus. From this study, we report two new, highly potent neutralizing antibodies, A9 and D6, against enterovirus 71 (EV71), the causative agent of HFMD. Both antibodies prevent the virus from entering the host cell, a step that is important for establishing a successful infection. A9 destabilizes and damages the virus capsid that forms an outer protective covering around the genome of the virus, while also interfering with virus attachment to the host cells. In contrast, D6 only prevents binding of the virus to its receptor(s). The mechanism of neutralization of A9 is unique and has not been observed before for neutralizing antibodies targeting EVs. The two antibodies that we are reporting in this study have potential to be developed into much-needed therapeutic interventions for treatment of HFMD, outbreaks of which are reported every year in the Asia-Pacific region. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 395.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.2 KB 15.2 KB | Display Display | ![]() |
Images | ![]() | 195.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 578.8 KB | Display | ![]() |
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Full document | ![]() | 578.4 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zudMC ![]() 6964C ![]() 5zufC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : COMPLEX OF EV71 AND D6 NEUTRALIZING ANTIBODY FAB
Entire | Name: COMPLEX OF EV71 AND D6 NEUTRALIZING ANTIBODY FAB |
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Components |
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-Supramolecule #1: COMPLEX OF EV71 AND D6 NEUTRALIZING ANTIBODY FAB
Supramolecule | Name: COMPLEX OF EV71 AND D6 NEUTRALIZING ANTIBODY FAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: D6 FAB GENERATED BY MICE AND CLEAVAGE BY ENZYME FROM ANTIBODY |
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-Supramolecule #2: EV71
Supramolecule | Name: EV71 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 / Details: capsid protein VP1,VP2,VP3 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: D6 NEUTRALIZING ANTIBODY FAB
Supramolecule | Name: D6 NEUTRALIZING ANTIBODY FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 / Details: antibodies |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 32.787902 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GDRVADVIES SIEDSSSRAL THALPAPTGQ NTQVSSHRLD TGKVPALQAA EIGASSNASD ESMIETRCVL NSHSTAETTL DSFFSRAGL VGEIDLPLKG TTNPNGYANW DIDITGYAQM RRKVELFTYM RFDAEFTFVA CTPTGEVVPQ LLQYMFVPPG A PKPDSRES ...String: GDRVADVIES SIEDSSSRAL 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 |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.874252 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.468225 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #4: R10 ANTIBODY LIGHT CHAIN
Macromolecule | Name: R10 ANTIBODY LIGHT CHAIN / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.283535 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DIVLTQSPAI MSASPGEKVT MTCSASSSVS YIHWYQQKSG TSPKRWIYDT SRLAFGVPGR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNYTFGGG TNLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN S WTDQDSKD ...String: DIVLTQSPAI MSASPGEKVT MTCSASSSVS YIHWYQQKSG TSPKRWIYDT SRLAFGVPGR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNYTFGGG TNLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN S WTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RNEC |
-Macromolecule #5: R10 ANTIBODY HEAVY CHAIN
Macromolecule | Name: R10 ANTIBODY HEAVY CHAIN / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.67165 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EVKLVESGGG SVKPGGSLKL SCAASGFSFS TYGMSWVRQT PEKRLEWVAT ISGGGGYTYY PDSVKGRFTI SRDNARNILY LQMSSLRSG DTAMYYCARR VTTVAEYYFD YWGQGTTLTV SSPKTTPPSV YPLAPAAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String: EVKLVESGGG SVKPGGSLKL SCAASGFSFS TYGMSWVRQT PEKRLEWVAT ISGGGGYTYY PDSVKGRFTI SRDNARNILY LQMSSLRSG DTAMYYCARR VTTVAEYYFD YWGQGTTLTV SSPKTTPPSV YPLAPAAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PR |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1500 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |