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- EMDB-33101: CVB5-intermediate altered particle containing VP1/VP2/VP3 and RNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-33101
TitleCVB5-intermediate altered particle containing VP1/VP2/VP3 and RNA genome
Map data
Sample
  • Virus: Coxsackievirus B5
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
KeywordsCoxsackie virus B5 / intermediate altered particle / 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 / viral capsid / 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 / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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
Similarity search - Component
Biological speciesCoxsackievirus B5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsYang P / Wang K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900873 China
CitationJournal: J Virol / Year: 2022
Title: Atomic Structures of Coxsackievirus B5 Provide Key Information on Viral Evolution and Survival.
Authors: Peng Yang / Dawei Shi / Jianmeng Fu / Li Zhang / Ruihong Chen / Binyang Zheng / Xiangxi Wang / Sihong Xu / Ling Zhu / Kang Wang /
Abstract: Coxsackie virus B5 (CVB5), a main serotype in human Enterovirus B (EVB), can cause severe viral encephalitis and aseptic meningitis among infants and children. Currently, there is no approved vaccine ...Coxsackie virus B5 (CVB5), a main serotype in human Enterovirus B (EVB), can cause severe viral encephalitis and aseptic meningitis among infants and children. Currently, there is no approved vaccine or antiviral therapy available against CVB5 infection. Here, we determined the atomic structures of CVB5 in three forms: mature full (F) particle (2.73 Å), intermediate altered (A) particle (2.81 Å), and procapsid empty (E) particle (2.95 Å). Structural analysis of F particle of CVB5 unveiled similar structures of "canyon," "puff," and "knob" as those other EV-Bs. We observed structural rearrangements that are alike during the transition from F to A particle, indicative of similar antigenicity, cell entry, and uncoating mechanisms shared by all EV-Bs. Further comparison of structures and sequences among all structure-known EV-Bs revealed that while the residues targeted by neutralizing MAbs are diversified and drive the evolution of EV-Bs, the relative conserved residues recognized by uncoating receptors could serve as the basis for the development of antiviral vaccines and therapeutics. As one of the main serotypes in Enterovirus B, CVB5 has been commonly reported in recent years. The atomic structures of CVB5 shown here revealed classical features found in EV-Bs and the structural rearrangement occurring during particle expansion and uncoating. Also, structure- and sequence-based comparison between CVB5 and other structure-known EV-Bs screened out key domains important for viral evolution and survival. All these provide insights into the development of vaccine and therapeutics for EV-Bs.
History
DepositionMar 20, 2022-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33101.png

Downloads & links

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Map

FileDownload / File: emd_33101.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 360 pix.
= 478.44 Å		1.33 Å/pix.
x 360 pix.
= 478.44 Å		1.33 Å/pix.
x 360 pix.
= 478.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.329 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0635
Minimum - Maximum-0.1663748 - 0.28729424
Average (Standard dev.)-0.000025619202 (±0.017866189)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 478.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Coxsackievirus B5

EntireName: Coxsackievirus B5
Components
  • Virus: Coxsackievirus B5
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein

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Supramolecule #1: Coxsackievirus B5

SupramoleculeName: Coxsackievirus B5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Coxsackievirus B5-A-particle / NCBI-ID: 12074 / Sci species name: Coxsackievirus B5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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 B5
Molecular weightTheoretical: 26.653973 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTRHVKNYHS RSESTVENFL CRSACVFYTT YRNHGTDGDN FGYWVISTRQ VAQLRRKLEM FTYARFDLEL TFVITSTQEQ STIQGQDSP VLTHQIMYVP PGGPVPTKVN SYSWQTSTNP SVFWTEGSAP PRMSIPFISI GNAYSMFYDG WAKFDKQGTY G INTLNNMG ...String:
QTRHVKNYHS RSESTVENFL CRSACVFYTT YRNHGTDGDN FGYWVISTRQ VAQLRRKLEM FTYARFDLEL TFVITSTQEQ STIQGQDSP VLTHQIMYVP PGGPVPTKVN SYSWQTSTNP SVFWTEGSAP PRMSIPFISI GNAYSMFYDG WAKFDKQGTY G INTLNNMG TLYMRHVNDG SPGPIVSTVR IYFKPKHVKT WVPRPPRLCQ YQKAGNVNFE PTGVTESRTD ITTMQ

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 B5
Molecular weightTheoretical: 27.242725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVRSITLGNS TITTQECANV VVGYGVWPTY LNDDEATAED QPTQPDVATC RFYTLESVMW QQSSPGWWWK FPDALSNMGL FGQNMQYHY LGRAGYTVHV QCNASKFHQG CLLVVCVPEA EMGCATLANK PDQKSLSNGE TANMFESQNS TGQTAVQANV I NAGMGVGV ...String:
RVRSITLGNS TITTQECANV VVGYGVWPTY LNDDEATAED QPTQPDVATC RFYTLESVMW QQSSPGWWWK FPDALSNMGL FGQNMQYHY LGRAGYTVHV QCNASKFHQG CLLVVCVPEA EMGCATLANK PDQKSLSNGE TANMFESQNS TGQTAVQANV I NAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHNNF TLMIIPFAPL SYSTGATTYV PITVTVAPMC AE YNGLRLA G

UniProtKB: Genome polyprotein

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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 B5
Molecular weightTheoretical: 26.163672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMDIPGQV NNLMEIAEVD SVVPVNNTEG KVLSIESYQI PVQSNSTNGS QVFGFPLMP GASSVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTTRKEAM LGTHVIWDVG L QSSCVLCI ...String:
GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMDIPGQV NNLMEIAEVD SVVPVNNTEG KVLSIESYQI PVQSNSTNGS QVFGFPLMP GASSVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTTRKEAM LGTHVIWDVG L QSSCVLCI PWISQTHYRY VVVDEYTAGG YITCWYQTNI VVPADTQSDC KILCFVSACN DFSVRMLKDT PFIKQDNFYQ

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

Concentration1.5 mg/mL
BufferpH: 7.4 / Details: PBS buffer
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 25 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1cov

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7675
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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