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- EMDB-30321: Coxsackievirus B5 (CVB5) F-particle -

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Basic information

Entry
Database: EMDB / ID: EMD-30321
TitleCoxsackievirus B5 (CVB5) F-particle
Map data
Sample
  • Virus: Coxsackievirus B5
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID
  • Ligand: MYRISTIC ACID
KeywordsEchovirus B / mature / 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 / viral capsid / 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 / VP4 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang K / Rao Z
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesKJZD-SW-L05 China
CitationJournal: Nat Commun / Year: 2020
Title: Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage.
Authors: Kang Wang / Ling Zhu / Yao Sun / Minhao Li / Xin Zhao / Lunbiao Cui / Li Zhang / George F Gao / Weiwei Zhai / Fengcai Zhu / Zihe Rao / Xiangxi Wang /
Abstract: Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor ...Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty- and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryo-electron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage.
History
DepositionJun 8, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
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: 0.048
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c9y
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c9y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30321.png

Downloads & links

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Map

FileDownload / File: emd_30321.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.)
1.35 Å/pix.
x 360 pix.
= 484.2 Å		1.35 Å/pix.
x 360 pix.
= 484.2 Å		1.35 Å/pix.
x 360 pix.
= 484.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.345 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.048
Minimum - Maximum-0.23249432 - 0.38257855
Average (Standard dev.)-0.00005105768 (±0.022410912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 484.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3451.3451.345
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z484.200484.200484.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-163-114-126
NX/NY/NZ210124170
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2320.383-0.000

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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: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID
  • Ligand: MYRISTIC ACID

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Supramolecule #1: Coxsackievirus B5

SupramoleculeName: Coxsackievirus B5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Particles purified from the cell cultures innoculated with the live CB5.
NCBI-ID: 12074 / Sci species name: Coxsackievirus B5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Diameter: 30.0 Å / T number (triangulation number): 3

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B5
Molecular weightTheoretical: 31.574322 KDa
SequenceString: GPTGEAVERA IARVADTIGS GPVNSESIPA LTAAETGHTS QVVPADTMQT RHVKNYHSRS ESTVENFLCR SACVFYTTYR NHGTDGDNF GYWVISTRQV AQLRRKLEMF TYARFDLELT FVITSTQEQS TIQGQDSPVL THQIMYVPPG GPVPTKVNSY S WQTSTNPS ...String:
GPTGEAVERA IARVADTIGS GPVNSESIPA LTAAETGHTS QVVPADTMQT RHVKNYHSRS ESTVENFLCR SACVFYTTYR NHGTDGDNF GYWVISTRQV AQLRRKLEMF TYARFDLELT FVITSTQEQS TIQGQDSPVL THQIMYVPPG GPVPTKVNSY S WQTSTNPS VFWTEGSAPP RMSIPFISIG NAYSMFYDGW AKFDKQGTYG INTLNNMGTL YMRHVNDGSP GPIVSTVRIY FK PKHVKTW VPRPPRLCQY QKAGNVNFEP TGVTESRTDI TTMQTT

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 B5
Molecular weightTheoretical: 28.626143 KDa
SequenceString: SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLNDDEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNM GLFGQNMQYH YLGRAGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLAN KPDQKSLSNG ETANMFESQN S TGQTAVQA ...String:
SPSAEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPT YLNDDEATAE DQPTQPDVAT CRFYTLESVM WQQSSPGWWW KFPDALSNM GLFGQNMQYH YLGRAGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLAN KPDQKSLSNG ETANMFESQN S TGQTAVQA NVINAGMGVG VGNLTIFPHQ WINLRTNNSA TIVMPYINSV PMDNMFRHNN FTLMIIPFAP LSYSTGATTY VP ITVTVAP MCAEYNGLRL AGKQ

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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 B5
Molecular weightTheoretical: 26.163672 KDa
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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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B5
Molecular weightTheoretical: 7.326025 KDa
SequenceString:
GAQVSTQKTG AHETGLSASG NSIIHYTNVN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM IKSMPALN

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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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Macromolecule #6: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC 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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 8890
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7c9y:
Coxsackievirus B5 (CVB5) F-particle

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