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- EMDB-34054: Cryo-EM structure of compact CA16 empty particle in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-34054
TitleCryo-EM structure of compact CA16 empty particle in complex with a neutralizing antibody 8C4
Map data
Sample
  • Complex: Cryo-EM structure of compact CA16 empty particle in complex with a neutralizing antibody 8C4
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Light chain of chain
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: The heavy chain of the antibody 8C4
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE
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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / 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
Similarity search - Function
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCong Y / Liu CX
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29040300 China
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of antibody neutralization of coxsackievirus A16.
Authors: Chao Zhang / Caixuan Liu / Jinping Shi / Yalei Wang / Cong Xu / Xiaohua Ye / Qingwei Liu / Xue Li / Weihua Qiao / Yannan Yin / Yao Cong / Zhong Huang /
Abstract: Coxsackievirus A16 (CVA16) causes hand, foot and mouth disease in infants and young children. However, no vaccine or anti-viral agent is currently available for CVA16. Here, the functions and working ...Coxsackievirus A16 (CVA16) causes hand, foot and mouth disease in infants and young children. However, no vaccine or anti-viral agent is currently available for CVA16. Here, the functions and working mechanisms of two CVA16-specific neutralizing monoclonal antibodies (MAbs), 9B5 and 8C4, are comprehensively investigated. Both 9B5 and 8C4 display potent neutralization in vitro and prophylactic and therapeutic efficacy in a mouse model of CVA16 infection. Mechanistically, 9B5 exerts neutralization primarily through inhibiting CVA16 attachment to cell surface via blockade of CVA16 binding to its attachment receptor, heparan sulfate, whereas 8C4 functions mainly at the post-attachment stage of CVA16 entry by interfering with the interaction between CVA16 and its uncoating receptor SCARB2. Cryo-EM studies show that 9B5 and 8C4 target distinct epitopes located at the 5-fold and 3-fold protrusions of CVA16 capsids, respectively, and exhibit differential binding preference to three forms of naturally occurring CVA16 particles. Moreover, 9B5 and 8C4 are compatible in formulating an antibody cocktail which displays the ability to prevent virus escape seen with individual MAbs. Together, our work elucidates the functional and structural basis of CVA16 antibody-mediated neutralization and protection, providing important information for design and development of effective CVA16 vaccines and antibody therapies.
History
DepositionAug 9, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34054.png

Downloads & links

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Map

FileDownload / File: emd_34054.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0018067906 - 1.780695
Average (Standard dev.)0.0067653926 (±0.060703423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 572.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of compact CA16 empty particle in complex with ...

EntireName: Cryo-EM structure of compact CA16 empty particle in complex with a neutralizing antibody 8C4
Components
  • Complex: Cryo-EM structure of compact CA16 empty particle in complex with a neutralizing antibody 8C4
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Light chain of chain
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: The heavy chain of the antibody 8C4
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE

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Supramolecule #1: Cryo-EM structure of compact CA16 empty particle in complex with ...

SupramoleculeName: Cryo-EM structure of compact CA16 empty particle in complex with a neutralizing antibody 8C4
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Coxsackievirus A16

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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: Coxsackievirus A16
Molecular weightTheoretical: 25.623205 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: HSTQETAIGN FFSRAGLVSI ITMPTMGTQN TDGYANWDID LMGYAQLRRK CELFTYMRFD AEFTFVVAKP NGELVPQLLQ YMYVPPGAP KPTSRDSFAW QTATNPSVFV KMTDPPAQVS VPFMSPASAY QWFYDGYPTF GEHLQANDLD YGQCPNNMMG T FSIRTVGT ...String:
HSTQETAIGN FFSRAGLVSI ITMPTMGTQN TDGYANWDID LMGYAQLRRK CELFTYMRFD AEFTFVVAKP NGELVPQLLQ YMYVPPGAP KPTSRDSFAW QTATNPSVFV KMTDPPAQVS VPFMSPASAY QWFYDGYPTF GEHLQANDLD YGQCPNNMMG T FSIRTVGT KKSPHSITLR VYMRIKHVRA WIPRPLRNQP YLFKTNPNYK GNDIKCTSTS RDKITTL

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Macromolecule #2: Light chain of chain

MacromoleculeName: Light chain of chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 23.619988 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: DIQMTQSSSY LSVSLGGRVT ITCKASDHIN NWLAWYQQKP GNAPRLLISG ATSLETGVPS RFSGSGSGKD YTLSITSLQT EDVATYYCQ QYWNSPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSSSY LSVSLGGRVT ITCKASDHIN NWLAWYQQKP GNAPRLLISG ATSLETGVPS RFSGSGSGKD YTLSITSLQT EDVATYYCQ QYWNSPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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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: Coxsackievirus A16
Molecular weightTheoretical: 33.77284 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: ENSNSASEGS TINYTTINYY KDAYAASAGR QDMSQDPKRF TDPVMDVIHE MAPPLKSPSA EACGYSDRVA QLTIGNSTIT TQEAANIVI AYGEWPEYCP DTDATAVDKP TRPDVSVNRF FTLDTKSWAK DSKGWYWKFP DVLTEVGVFG QNAQFHYLYR S GFCVHVQC ...String:
ENSNSASEGS TINYTTINYY KDAYAASAGR QDMSQDPKRF TDPVMDVIHE MAPPLKSPSA EACGYSDRVA QLTIGNSTIT TQEAANIVI AYGEWPEYCP DTDATAVDKP TRPDVSVNRF FTLDTKSWAK DSKGWYWKFP DVLTEVGVFG QNAQFHYLYR S GFCVHVQC NASKFHQGAL LVAVLPEYVL GTIAGGTGNE NSHPPYATTQ PGQVGAVLTH PYVLDAGIPL SQLTVCPHQW IN LRTNNCA TIIVPYMNTV PFDSALNHCN FGLLVIPVVP LDFNAGATSE IPITVTIAPM CAEFAGLRQA VKQ

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Macromolecule #4: The heavy chain of the antibody 8C4

MacromoleculeName: The heavy chain of the antibody 8C4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 22.743381 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: QVQLQQSGPE LVKPGASVKI SCKASGYAFS TSWMNWVIQR PGQGLEWIGR IYPGDGDTNY NGKFKGKATL TADKSSSTAY MQLSSLTSV DSAVYFCARR DYGYFDYWGQ GTTLTVSSAK TTPPSVYPLA PGCGDTTGSS VTLGCLVKGY FPESVTVTWN S GSLSSSVH ...String:
QVQLQQSGPE LVKPGASVKI SCKASGYAFS TSWMNWVIQR PGQGLEWIGR IYPGDGDTNY NGKFKGKATL TADKSSSTAY MQLSSLTSV DSAVYFCARR DYGYFDYWGQ GTTLTVSSAK TTPPSVYPLA PGCGDTTGSS VTLGCLVKGY FPESVTVTWN S GSLSSSVH TFPALLQSGL YTMSSSVTVP SSTWPSQTVT CSVAHPASST TVDKKL

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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 / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 26.646318 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV RNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GSVPADRITA MLGTHVIWDF G LQSSVTLV ...String:
GIPTELKPGT NQFLTTDDGV SAPILPGFHP TPPIHIPGEV RNLLEICRVE TILEVNNLKT NETTPMQRLC FPVSVQSKTG ELCAAFRAD PGRDGPWQST ILGQLCRYYT QWSGSLEVTF MFAGSFMATG KMLIAYTPPG GSVPADRITA MLGTHVIWDF G LQSSVTLV VPWISNTHYR AHARAGYFDY YTTGIITIWY QTNYVVPIGA PTTAYIVALA AAQDNFTMKL CKDTEDIEQT AN IQ

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Macromolecule #6: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20196

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