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- PDB-7thx: Cryo-EM structure of W6 possum enterovirus -

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Basic information

Entry
Database: PDB / ID: 7thx
TitleCryo-EM structure of W6 possum enterovirus
Components(Capsid protein ...) x 4
KeywordsVIRUS / enterovirus / icosahedral
Function / homology: / SPHINGOSINE
Function and homology information
Biological speciesPossum enterovirus W6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWang, I. / Jayawardena, N. / Strauss, M. / Bostina, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPAS/00011-2020 Canada
CitationJournal: Viruses / Year: 2022
Title: Cryo-EM Structure of a Possum Enterovirus.
Authors: Ivy Wang / Sandeep K Gupta / Guillaume Ems / Nadishka Jayawardena / Mike Strauss / Mihnea Bostina /
Abstract: Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess ...Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clear, with the entrance to the pocket being smaller than for other enteroviruses.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Refinement description / Category: pdbx_initial_refinement_model / refine / Item: _refine.ls_d_res_high
Revision 1.2Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-25905
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8586
Polymers91,5204
Non-polymers3392
Water37821
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,511,504360
Polymers5,491,189240
Non-polymers20,315120
Water2,162120
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 459 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)459,29230
Polymers457,59920
Non-polymers1,69310
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 551 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)551,15036
Polymers549,11924
Non-polymers2,03212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Capsid protein ... , 4 types, 4 molecules 1234

#1: Protein Capsid protein VP1


Mass: 30311.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6
#2: Protein Capsid protein VP2


Mass: 26577.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6
#3: Protein Capsid protein VP3


Mass: 26997.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6
#4: Protein Capsid protein VP4


Mass: 7632.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Possum enterovirus W6

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Non-polymers , 3 types, 23 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Possum enterovirus W6
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Possum enterovirus W6
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.37 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.9image acquisition
4CTFFIND4.08CTF correction
7UCSF Chimeramodel fitting
12RELION3.13D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9687 / Details: relion 3.1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 5OSN

5osn


Accession code: 5OSN / Source name: PDB / Type: experimental model
RefinementResolution: 2.96→114.838 Å / Cor.coef. Fo:Fc: 0.745 / WRfactor Rwork: 0.271 / SU B: 13.188 / SU ML: 0.224 / Average fsc overall: 0.9236 / Average fsc work: 0.9236 / ESU R: 0.321
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.2714 66237 -
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 29.726 Å2
Refinement stepCycle: 1 / Total: 37770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.0136226
ELECTRON MICROSCOPYr_bond_other_d00.0155742
ELECTRON MICROSCOPYr_angle_refined_deg1.981.6518499
ELECTRON MICROSCOPYr_angle_other_deg1.3491.5713205
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.8195772
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.18222.372312
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.53315939
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.6371534
ELECTRON MICROSCOPYr_chiral_restr0.090.2834
ELECTRON MICROSCOPYr_gen_planes_refined0.010.027126
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021484
ELECTRON MICROSCOPYr_nbd_refined0.1650.21436
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1640.28832
ELECTRON MICROSCOPYr_nbtor_refined0.1630.25732
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0820.26058
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.120.296
ELECTRON MICROSCOPYr_metal_ion_refined0.0480.22
ELECTRON MICROSCOPYr_mcbond_it3.5682.8123100
ELECTRON MICROSCOPYr_mcbond_other3.5622.8093099
ELECTRON MICROSCOPYr_mcangle_it6.094.2123868
ELECTRON MICROSCOPYr_mcangle_other6.0924.2153869
ELECTRON MICROSCOPYr_scbond_it6.013.4473126
ELECTRON MICROSCOPYr_scbond_other6.0093.4523127
ELECTRON MICROSCOPYr_scangle_it10.2954.9014631
ELECTRON MICROSCOPYr_scangle_other10.2944.9054632
ELECTRON MICROSCOPYr_lrange_it16.1353.98321588
ELECTRON MICROSCOPYr_lrange_other16.09753.96321581
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.1-3.180.56848630.56848630.780.568
3.18-3.2680.41447970.41447970.8470.414
3.268-3.3620.33546220.33546220.8790.335
3.362-3.4660.27445940.27445940.910.274
3.466-3.5790.23543430.23543430.930.235
3.579-3.7050.21541980.21541980.9450.215
3.705-3.8440.2141130.2141130.9520.21
3.844-4.0010.21238850.21238850.960.212
4.001-4.1790.20838200.20838200.9680.208
4.179-4.3820.21435370.21435370.970.214
4.382-4.6190.21534600.21534600.9730.215
4.619-4.8990.20132440.20132440.9730.201
4.899-5.2360.18130520.18130520.9710.181
5.236-5.6550.18127960.18127960.9620.181
5.655-6.1930.21825830.21825830.9460.218
6.193-6.9220.25223920.25223920.9330.252
6.922-7.9880.3220480.3220480.9090.32
7.988-9.7710.34817820.34817820.9080.348
9.771-13.7690.44713510.44713510.9150.447
13.769-114.8381.2317571.2317570.9521.231

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