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- EMDB-31044: Echovirus3 empty compacted particle -

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Basic information

Entry
Database: EMDB / ID: EMD-31044
TitleEchovirus3 empty compacted particle
Map data
Sample
  • Virus: Echovirus E3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE
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 / 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
Biological speciesEchovirus E3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFeng R
CitationJournal: Cell Discov / Year: 2021
Title: Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody.
Authors: Rui Feng / Lei Wang / Dawei Shi / Binyang Zheng / Li Zhang / Hai Hou / Deju Xia / Lunbiao Cui / Xiangxi Wang / Sihong Xu / Kang Wang / Ling Zhu /
History
DepositionMar 7, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eai
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eai
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31044.png

Downloads & links

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Map

FileDownload / File: emd_31044.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 431.04 Å		1.35 Å/pix.
x 320 pix.
= 431.04 Å		1.35 Å/pix.
x 320 pix.
= 431.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.347 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06420568 - 0.12306498
Average (Standard dev.)0.0014883344 (±0.009967008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 431.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3471.3471.347
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z431.040431.040431.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0640.1230.001

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Supplemental data

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Sample components

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Entire : Echovirus E3

EntireName: Echovirus E3
Components
  • Virus: Echovirus E3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE

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Supramolecule #1: Echovirus E3

SupramoleculeName: Echovirus E3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 47516 / Sci species name: Echovirus E3 / Virus type: VIRION / Virus isolate: SEROTYPE / 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 E3
Molecular weightTheoretical: 32.801801 KDa
SequenceString: GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP ...String:
GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP SIFWTEGCAP ARMSVPFISI GNAYSNFYDG WSHFTQEGVY GFNSLNNMGH IYVRHVNEQS LGVSTSTLRV YF KPKHVRA WVPRPPRLSP YVKSSNVNFK PTAVTTERKD INDVGTLRPV GYTNH

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Macromolecule #2: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E3
Molecular weightTheoretical: 36.605734 KDa
SequenceString: GAQVSTQKTG AHETSLTASG NSTIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPMKDVM IKSLPALNSP TVEECGFSDR VRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL F GQNMEYHY ...String:
GAQVSTQKTG AHETSLTASG NSTIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPMKDVM IKSLPALNSP TVEECGFSDR VRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL F GQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV YN AGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHYNF TLMIIPFAKL EYTEQASNYV PITVTVAPMC AEY NGLRLA SHQ

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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 E3
Molecular weightTheoretical: 26.264879 KDa
SequenceString: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI ...String:
GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG YVTCWYQTGL IVPPGAPPSC TILCFASACN DFSVRNLRDT PFIEQTQLLQ

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Macromolecule #4: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 4 / 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 TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2330
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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