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- PDB-7opx: CryoEM structure of human enterovirus 70 native virion -

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Basic information

Entry
Database: PDB / ID: 7opx
TitleCryoEM structure of human enterovirus 70 native virion
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / EV70 / enterovirus 70 / virion / native
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 / 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 / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / 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 / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 speciesHuman enterovirus 70
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsFuzik, T. / Plevka, P. / Moravcova, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
CitationJournal: J Virol / Year: 2022
Title: Structure of Human Enterovirus 70 and Its Inhibition by Capsid-Binding Compounds.
Authors: Tibor Füzik / Jana Moravcová / Sergei Kalynych / Pavel Plevka /
Abstract: Enterovirus 70 (EV70) is a human pathogen belonging to the family . EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of ...Enterovirus 70 (EV70) is a human pathogen belonging to the family . EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of the disease caused by EV70, its structure is unknown. Here, we present the structures of the EV70 virion, altered particle, and empty capsid determined by cryo-electron microscopy. The capsid of EV70 is composed of the subunits VP1, VP2, VP3, and VP4. The partially collapsed hydrophobic pocket located in VP1 of the EV70 virion is not occupied by a pocket factor, which is commonly present in other enteroviruses. Nevertheless, we show that the pocket can be targeted by the antiviral compounds WIN51711 and pleconaril, which block virus infection. The inhibitors prevent genome release by stabilizing EV70 particles. Knowledge of the structures of complexes of EV70 with inhibitors will enable the development of capsid-binding therapeutics against this virus. Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The discharge from infected eyes enables the high-efficiency transmission of EV70 in overcrowded areas with low hygienic standards. Currently, only symptomatic treatments are available. We determined the structures of EV70 in its native form, the genome release intermediate, and the empty capsid resulting from genome release. Furthermore, we elucidated the structures of EV70 in complex with two inhibitors that block virus infection, and we describe the mechanism of their binding to the virus capsid. These results enable the development of therapeutics against EV70.
History
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)95,4904
Polymers95,4904
Non-polymers00
Water2,702150
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,729,412240
Polymers5,729,412240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1generate(1), (1), (1)
2generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
3generate(1), (-1), (-1)
4generate(0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5)
5generate(0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017)
6generate(-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017)
7generate(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
8generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
9generate(-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017)
10generate(0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017)
11generate(-1), (-1), (1)
12generate(-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017)
13generate(-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017)
14generate(-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017)
15generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
16generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
17generate(-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017)
18generate(-1), (1), (-1)
19generate(-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017)
20generate(-1), (1), (-1)
21generate(-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5)
22generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
23generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
24generate(0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017)
25generate(-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5)
26generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017)
27generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
28generate(1), (-1), (-1)
29generate(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
30generate(0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017)
31generate(-1), (1), (-1)
32generate(0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5)
33generate(-1), (-1), (1)
34generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
35generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
36generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
37generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
38generate(0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5)
39generate(0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017)
40generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
41generate(1), (-1), (-1)
42generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
43generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
44generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
45generate(0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5)
46generate(-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017)
47generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
48generate(1), (1), (1)
49generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
50generate(1), (1), (1)
51generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
52generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
53generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
54generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
55generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
56generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)
57generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
58generate(-1), (-1), (1)
59generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
60generate(-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017)

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Components

#1: Protein Capsid protein VP1 /


Mass: 34049.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 70 (strain J670/71) / Cell line: hTERT RPE1 / Strain: J670/71 / References: UniProt: P32537
#2: Protein Capsid protein VP2 /


Mass: 27536.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 70 (strain J670/71) / Cell line: hTERT RPE1 / Strain: J670/71 / References: UniProt: P32537
#3: Protein Capsid protein VP3 /


Mass: 26717.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 70 (strain J670/71) / Cell line: hTERT RPE1 / Strain: J670/71 / References: UniProt: P32537
#4: Protein Capsid protein VP4 /


Mass: 7186.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 70 (strain J670/71) / Cell line: hTERT RPE1 / Strain: J670/71 / References: UniProt: P32537
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus D70 / Type: VIRUS / Details: isolated from infected hTERT RPE1 cells / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 5.7 MDa / Experimental value: NO
Source (natural)Organism: Human enterovirus 70 (strain J670/71)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellName: Capsid / Diameter: 330 nm / Triangulation number (T number): 1
Buffer solutionpH: 7
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6698
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1crYOLO1.5particle selection
2EPU1.8image acquisition
4GctfCTF correctioninitial CTF estimation
5RELION3.1CTF correctionCTF refinement and correction
8UCSF Chimeramodel fitting
9Cootmodel fitting
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
15PHENIXmodel refinement
16REFMACmodel refinement
Image processingDetails: Movie frames motion correction (MotionCor2)
CTF correctionDetails: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10524 / Details: autopicking using crYOLO
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6390 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 43 / Protocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 4MW8

4mw8


Pdb chain-ID: A
RefinementResolution: 2.63→340.16 Å / Cor.coef. Fo:Fc: 0.83 / SU B: 7.765 / SU ML: 0.149 / ESU R: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31343 --
obs0.31343 384381 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.974 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Total: 6452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0180.0136458
ELECTRON MICROSCOPYr_bond_other_d0.0350.0176007
ELECTRON MICROSCOPYr_angle_refined_deg1.7721.6448799
ELECTRON MICROSCOPYr_angle_other_deg2.2871.5713837
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.3245806
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.79323.087311
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.725151038
ELECTRON MICROSCOPYr_dihedral_angle_4_deg22.2361530
ELECTRON MICROSCOPYr_chiral_restr0.0960.2880
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.027367
ELECTRON MICROSCOPYr_gen_planes_other0.0130.021497
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it32.7122.93236
ELECTRON MICROSCOPYr_mcbond_other32.7192.8983235
ELECTRON MICROSCOPYr_mcangle_it34.4724.8994038
ELECTRON MICROSCOPYr_mcangle_other34.4694.9014039
ELECTRON MICROSCOPYr_scbond_it38.0353.9063222
ELECTRON MICROSCOPYr_scbond_other38.033.9083223
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other40.7985.4224762
ELECTRON MICROSCOPYr_long_range_B_refined51.25755.6317376
ELECTRON MICROSCOPYr_long_range_B_other51.25355.6467377
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.595 28265 -
obs--100 %

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