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- EMDB-0854: Cryo-EM structure of full echovirus 11 particle at pH 7.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-0854
TitleCryo-EM structure of full echovirus 11 particle at pH 7.4
Map dataCryo-EM structure of full echovirus 11 particle at pH 7.4
Sample
  • Virus: Echovirus E11
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Protein or peptide: Capsid protein VP1
  • Ligand: SPHINGOSINE
KeywordsCryo-EM structure / echovirus 11 / full particle / pH 7.4 / 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 suppression of host gene expression / 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 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E11
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsLiu S / Gao FG
CitationJournal: Chin.Sci.Bull. / Year: 2020
Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn.
Authors: Niu S / Liu C / Liu C / Liu S / Song Y / Zhang Y / Tian W / Zhao X / Wang P / Gao FG
History
DepositionNov 11, 2019-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6la3
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6la3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0854.png

Downloads & links

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Map

FileDownload / File: emd_0854.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of full echovirus 11 particle at pH 7.4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.05053587 - 0.12964413
Average (Standard dev.)-0.00046287462 (±0.0107418345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z418.560418.560418.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0510.130-0.000

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Supplemental data

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Sample components

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Entire : Echovirus E11

EntireName: Echovirus E11
Components
  • Virus: Echovirus E11
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Protein or peptide: Capsid protein VP1
  • Ligand: SPHINGOSINE

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Supramolecule #1: Echovirus E11

SupramoleculeName: Echovirus E11 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#4 / NCBI-ID: 12078 / Sci species name: Echovirus E11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 32.277359 KDa
SequenceString: VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI ...String:
VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI FWTEGNAPPR MSIPFISIGN AYSNFYDGWS HFSQNGVYGY NTLNHMGQIY VRHVNGSSPL PMTSTVRMYF KP KHVKVWV PRPPRLCQYK NASTVNFTPT NITEKRQSIN YIPETVKP

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 27.968449 KDa
SequenceString: DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG ...String:
DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG VGNLTIFPHQ WINLRTNNCA TIVMPYINNV PMDNMFRHHN FTLMIIPFVP LDYSSDSSTY VPITVTVAPM CA EYNGLRL ATSL

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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
Source (natural)Organism: Echovirus E11
Molecular weightTheoretical: 26.062578 KDa
SequenceString: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI ...String:
GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG NVTCWYQTGI VVPAGTPTSC SIMCFVSACN DFSVRLLKDT PFIEQSALLQ

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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: Echovirus E11
Molecular weightTheoretical: 7.495273 KDa
SequenceString:
MGAQVSTQKT GAHETGLNAS GRSIIHYTNI NYYKDAASNS ANRQDFSQDP GKFTEPVKDI MVKSLPALN

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Macromolecule #5: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 5 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.025 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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