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- EMDB-32997: Cryo-EM structure of Coxsackievirus B1 empty particle in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32997
TitleCryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (CVB1-E:9A3)
Map data
Sample
  • Complex: Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (CVB1-E:9A3)
    • Protein or peptide: 9A3 heavy chain
    • Protein or peptide: 9A3 light chain
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
KeywordsCoxsackievirus B1 / Neutralizing antibody / Cryo-EM / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 RIG-I 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 / DNA replication / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 VP4 superfamily / 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 VP4 superfamily / 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 / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsZheng Q / Zhu R / Sun H / Cheng T / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2022
Title: Structural basis for the synergistic neutralization of coxsackievirus B1 by a triple-antibody cocktail.
Authors: Qingbing Zheng / Rui Zhu / Zhichao Yin / Longfa Xu / Hui Sun / Hai Yu / Yuanyuan Wu / Yichao Jiang / Qiongzi Huang / Yang Huang / Dongqing Zhang / Liqin Liu / Hongwei Yang / Maozhou He / ...Authors: Qingbing Zheng / Rui Zhu / Zhichao Yin / Longfa Xu / Hui Sun / Hai Yu / Yuanyuan Wu / Yichao Jiang / Qiongzi Huang / Yang Huang / Dongqing Zhang / Liqin Liu / Hongwei Yang / Maozhou He / Zhenhong Zhou / Yanan Jiang / Zhenqin Chen / Huan Zhao / Yuqiong Que / Zhibo Kong / Lizhi Zhou / Tingting Li / Jun Zhang / Wenxin Luo / Ying Gu / Tong Cheng / Shaowei Li / Ningshao Xia /
Abstract: Coxsackievirus B1 (CVB1) is an emerging pathogen associated with severe neonatal diseases including aseptic meningitis, myocarditis, and pancreatitis and also with the development of type 1 diabetes. ...Coxsackievirus B1 (CVB1) is an emerging pathogen associated with severe neonatal diseases including aseptic meningitis, myocarditis, and pancreatitis and also with the development of type 1 diabetes. We characterize the binding and therapeutic efficacies of three CVB1-specific neutralizing antibodies (nAbs) identified for their ability to inhibit host receptor engagement. High-resolution cryo-EM structures showed that these antibodies recognize different epitopes but with an overlapping region in the capsid VP2 protein and specifically the highly variable EF loop. Moreover, they perturb capsid-receptor interactions by binding various viral particle forms. Antibody combinations achieve synergetic neutralization via a stepwise capsid transition and virion disruption, indicating dynamic changes in the virion in response to multiple nAbs targeting the receptor-binding site. Furthermore, this three-antibody cocktail protects against lethal challenge in neonatal mice and limits pancreatitis and viral replication in a non-obese diabetic mouse model. These results illustrate the utility of nAbs for rational design of therapeutics against picornaviruses such as CVB.
History
DepositionMar 1, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32997.png

Downloads & links

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Map

FileDownload / File: emd_32997.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 600 pix.
= 670.2 Å		1.12 Å/pix.
x 600 pix.
= 670.2 Å		1.12 Å/pix.
x 600 pix.
= 670.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.117 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.7
Minimum - Maximum-28.386399999999998 - 46.198086000000004
Average (Standard dev.)-0.026972499 (±2.4384825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 670.2 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 Coxsackievirus B1 empty particle in complex ...

EntireName: Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (CVB1-E:9A3)
Components
  • Complex: Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (CVB1-E:9A3)
    • Protein or peptide: 9A3 heavy chain
    • Protein or peptide: 9A3 light chain
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3

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Supramolecule #1: Cryo-EM structure of Coxsackievirus B1 empty particle in complex ...

SupramoleculeName: Cryo-EM structure of Coxsackievirus B1 empty particle in complex with nAb 9A3 (CVB1-E:9A3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Coxsackievirus B1

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Macromolecule #1: 9A3 heavy chain

MacromoleculeName: 9A3 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.768251 KDa
SequenceString:
EVKLVESGGG LVQPGGSLSL SCAASGFTFT DYYMNWVRQP SGKALEWLGF LRNKANGYTT EYSASVKGRF TISRDNSQSI LYLQMNALR AEDSATYYCA RSRYYGGTYR YALDYWGQGT SVTVS

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Macromolecule #2: 9A3 light chain

MacromoleculeName: 9A3 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.47268 KDa
SequenceString:
ENVLTQSPPI MSASPGEKVT MTCRASSSVS SSYLHWYQQK SGASPKLWIY STSNLASGVP ARFSGSGSGT SYSLTISSVE AEDAATYYC QQFSGYPLTF GAGTKLELK

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Macromolecule #3: Virion protein 1

MacromoleculeName: Virion protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 31.207117 KDa
SequenceString: GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF ...String:
GPVEESVDRA VARVADTISS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR SACVYYATYT NNSKKGFAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA SSVDAPVQTH QIMYVPPGGP VPTKVKDYAW Q TSTNPSVF WTEGNAPPRM SIPFISIGNA YSCFYDGWTQ FSRNGVYGIN TLNNMGTLYM RHVNEAGQGP IKSTVRIYFK PK HVKAWVP RPPRLCQYEK QKNVNFSPIG VTTSRTDIIT T

UniProtKB: Genome polyprotein

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Macromolecule #4: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 29.122744 KDa
SequenceString: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV ...String:
SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFSELSGG DSARMFTDTQ V GESNAKKV QTAVWNAGMG VGVGNLTIFP HQWINLRTNN SATLVMPYIN SVPMDNMFRH NNLTLMIIPF VPLNYSEGSS PY VPITVTI APMCAEYNGL RLASNQ

UniProtKB: Genome polyprotein

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Macromolecule #5: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 26.328764 KDa
SequenceString: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVEDEYTAAG YVTCWYQTNI VVPADVQSSC DILCFVSACN DFSVRMLKDT PFIRQDTFYQ

UniProtKB: Genome polyprotein

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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 TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10464
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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