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- EMDB-34062: Cryo-EM structure of compact coxsackievirus A16 empty particle in... -

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Basic information

Entry
Database: EMDB / ID: EMD-34062
TitleCryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5
Map data
Sample
  • Complex: Cryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: The light chain of the antibody 9B5
    • Protein or peptide: The heavy chain of the antibody 9B5
  • Ligand: SPHINGOSINE
Keywordscoxsackievirus A16 / antibody 9B5 / cryo-EM / STRUCTURAL PROTEIN
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 / nucleoside-triphosphate phosphatase ...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 / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion 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 (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 / 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
Similarity search - Component
Biological speciesCoxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 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 10, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34062.png

Downloads & links

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Map

FileDownload / File: emd_34062.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 520 pix.
= 572. Å		1.1 Å/pix.
x 520 pix.
= 572. Å		1.1 Å/pix.
x 520 pix.
= 572. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0015506492 - 1.7377009
Average (Standard dev.)0.006383835 (±0.05924825)
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 coxsackievirus A16 empty particle in...

EntireName: Cryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5
Components
  • Complex: Cryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: The light chain of the antibody 9B5
    • Protein or peptide: The heavy chain of the antibody 9B5
  • Ligand: SPHINGOSINE

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Supramolecule #1: Cryo-EM structure of compact coxsackievirus A16 empty particle in...

SupramoleculeName: Cryo-EM structure of compact coxsackievirus A16 empty particle in complex with a neutralizing antibody 9B5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Coxsackievirus A16

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 33.080402 KDa
Recombinant expressionOrganism: Mus sp. (mice)
SequenceString: GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTMG TQNTDGYANW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGELVPQ LLQYMYVPPG A PKPTSRDS ...String:
GDPIADMIDQ TVNNQVNRSL TALQVLPTAA NTEASSHRLG TGVVPALQAA ETGASSNASD KNLIETRCVL NHHSTQETAI GNFFSRAGL VSIITMPTMG TQNTDGYANW DIDLMGYAQL RRKCELFTYM RFDAEFTFVV AKPNGELVPQ LLQYMYVPPG A PKPTSRDS FAWQTATNPS VFVKMTDPPA QVSVPFMSPA SAYQWFYDGY PTFGEHLQAN DLDYGQCPNN MMGTFSIRTV GT KKSPHSI TLRVYMRIKH VRAWIPRPLR NQPYLFKTNP NYKGNDIKCT STSRDKITTL

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: 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

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / 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

UniProtKB: Genome polyprotein

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Macromolecule #4: The light chain of the antibody 9B5

MacromoleculeName: The light chain of the antibody 9B5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 23.600934 KDa
Recombinant expressionOrganism: Cercopithecus (mammal)
SequenceString: DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA ATNLADGVPS RFSGSGSGTQ YSLKINSLQS EDFGTYYCQ QFWDTPFTFG SGTKLAIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA ATNLADGVPS RFSGSGSGTQ YSLKINSLQS EDFGTYYCQ QFWDTPFTFG SGTKLAIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #5: The heavy chain of the antibody 9B5

MacromoleculeName: The heavy chain of the antibody 9B5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus A16
Molecular weightTheoretical: 23.500203 KDa
Recombinant expressionOrganism: Cercopithecus (mammal)
SequenceString: EVQLQQSGPE LVKPGASVKM SCKTSGYTFT ENTMHWVRQS HGKSLEWIGG IYPKNDDTKY NQKFKGKATL TVDKSSSTAC MELRSLTSE DSAVYYCARG DYENYFYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS ...String:
EVQLQQSGPE LVKPGASVKM SCKTSGYTFT ENTMHWVRQS HGKSLEWIGG IYPKNDDTKY NQKFKGKATL TVDKSSSTAC MELRSLTSE DSAVYYCARG DYENYFYAMD YWGQGTSVTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS SSVHTFPALL QSGLYTMSSS VTVPSSTWPS QTVTCSVAHP ASSTTVDKKL

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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

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13951
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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