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- EMDB-30805: Cryo-EM structure of Coxsackievirus B1 mature virion -

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Entry
Database: EMDB / ID: EMD-30805
TitleCryo-EM structure of Coxsackievirus B1 mature virion
Map dataCryo-EM structure of Coxsackievirus B1 mature virion
Sample
  • Virus: Coxsackievirus B1
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: PALMITIC ACID
KeywordsCoxsackievirus B1 / mature virion / 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 / symbiont-mediated suppression of host gene expression ...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 / symbiont-mediated suppression of host gene expression / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / 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 / cytoplasm
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 / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng Q / Li S
CitationJournal: Cell Host Microbe / Year: 2021
Title: Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating.
Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing ...Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing Zhang / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Lisheng Yang / Che Liu / Yuqiong Que / Mujin Fang / Ying Gu / Jun Zhang / Wenxin Luo / Z Hong Zhou / Shaowei Li / Tong Cheng / Ningshao Xia /
Abstract: Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a ...Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a hydrophobic pocket formed by the major viral capsid protein, VP1. Coxsackievirus and adenovirus receptor (CAR) is a universal uncoating receptor of group B coxsackieviruses (CVB). Here, we present five high-resolution cryoEM structures of CVB representing different stages of virus infection. Structural comparisons show that the CAR penetrates deeper into the canyon than other uncoating receptors, leading to a cascade of events: collapse of the VP1 hydrophobic pocket, high-efficiency release of the pocket factor and viral uncoating and genome release under neutral pH, as compared with low pH. Furthermore, we identified a potent therapeutic antibody that can neutralize viral infection by interfering with virion-CAR interactions, destabilizing the capsid and inducing virion disruption. Together, these results define the structural basis of CVB cell entry and antibody neutralization.
History
DepositionDec 18, 2020-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.1
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  • Surface view with fitted model
  • Atomic models: PDB-7dpf
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dpf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30805.png

Downloads & links

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Map

FileDownload / File: emd_30805.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Coxsackievirus B1 mature virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 400 pix.
= 451.2 Å		1.13 Å/pix.
x 400 pix.
= 451.2 Å		1.13 Å/pix.
x 400 pix.
= 451.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.29218066 - 0.43074647
Average (Standard dev.)0.0018679288 (±0.027760152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 451.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z451.200451.200451.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2920.4310.002

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Supplemental data

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Sample components

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Entire : Coxsackievirus B1

EntireName: Coxsackievirus B1
Components
  • Virus: Coxsackievirus B1
    • Protein or peptide: Virion protein 1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: PALMITIC ACID

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Supramolecule #1: Coxsackievirus B1

SupramoleculeName: Coxsackievirus B1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 12071 / Sci species name: Coxsackievirus B1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Virion protein 1

MacromoleculeName: Virion protein 1 / type: protein_or_peptide / ID: 1 / 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 #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / 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 #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
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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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1
Molecular weightTheoretical: 7.484246 KDa
SequenceString:
MGAQVSTQKT GAHETGLNAS GNSVIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MVKTMPALN

UniProtKB: Genome polyprotein

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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 III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35999
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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