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- PDB-3jbf: Complex of poliovirus with VHH PVSP19B -

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Basic information

Entry
Database: PDB / ID: 3jbf
TitleComplex of poliovirus with VHH PVSP19B
Components
  • (Capsid protein ...) x 4
  • nanobody VHH PVSP19B
KeywordsVIRUS/IMMUNE SYSTEM / poliovirus / nanobodies / VHH / neutralizing antibodies / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / 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) / Peptidase C3A/C3B, picornaviral ...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. / 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
PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Human poliovirus 1 Mahoney
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsStrauss, M. / Schotte, L. / Thys, B. / Filman, D.J. / Hogle, J.M.
CitationJournal: J Virol / Year: 2016
Title: Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.
Authors: Mike Strauss / Lise Schotte / Bert Thys / David J Filman / James M Hogle /
Abstract: Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In ...Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion.
IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five ...IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-6434
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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
7: nanobody VHH PVSP19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9086
Polymers111,6525
Non-polymers2561
Water00
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
7: nanobody VHH PVSP19B
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,714,483360
Polymers6,699,097300
Non-polymers15,38560
Water0
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
7: nanobody VHH PVSP19B
hetero molecules
x 5


  • icosahedral pentamer
  • 560 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)559,54030
Polymers558,25825
Non-polymers1,2825
Water0
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
7: nanobody VHH PVSP19B
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 671 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)671,44836
Polymers669,91030
Non-polymers1,5396
Water0
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 / P1D / Virion protein 1


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26419.352 Da / Num. of mol.: 1 / Fragment: UNP residues 342-578 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 7603.405 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300

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Antibody / Non-polymers , 2 types, 2 molecules 7

#5: Antibody nanobody VHH PVSP19B


Mass: 14064.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid details: pHEN6(c) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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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

Component
IDNameTypeDetailsParent-ID
1Nanobody PVSS8A in complex with poliovirus P1/MahoneyCOMPLEX60 nanobody VHH monomers bind to each poliovirion0
2Human poliovirus 1VIRUS1
3PVSP19B1
Molecular weightValue: 9 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 145 mM NaCl, 50 mM Na2HPO4.12H2O / pH: 7.4 / Details: 145 mM NaCl, 50 mM Na2HPO4.12H2O
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-flat 1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 154 K
Details: Blotted for 4 seconds before plunging into liquid ethane (homemade plunger).
Method: 4 second blot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Nov 27, 2013 / Details: Gatan K2 operated in Super-resolution mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELD / Nominal magnification: 23000 X / Calibrated magnification: 25381 X / Nominal defocus max: -4000 nm / Nominal defocus min: -1400 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polara holder / Temperature: 80 K / Temperature (max): 110 K / Temperature (min): 80 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 300

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Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2REFMAC5model fitting
3SPDBVmodel fitting
4FREALIGN3D reconstruction
CTF correctionDetails: per particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18009 / Nominal pixel size: 0.985 Å / Actual pixel size: 0.985 Å
Details: (Single particle details: The particles were processed using Frealign.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Target criteria: ML agreement with Fourier amplitudes and phases
Details: REFINEMENT PROTOCOL--flexible DETAILS--Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all ...Details: REFINEMENT PROTOCOL--flexible DETAILS--Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all neighbors present was built and refined to fit the corresponding subset of the experimental map. Portions of the model whose density resembled a structural homolog were identified and restrained to agree with the homolog. Detailed atomic models were constructed in areas of difference wherever the resolution of the map permitted. The Fourier-amplitude-weighted average cosine of the phase discrepancy was tracked.
Atomic model buildingPDB-ID: 1I3U

1i3u

RefinementResolution: 4.6→95.15 Å / Cor.coef. Fo:Fc: 0.702 / SU B: 110.77 / SU ML: 1.342 / σ(F): 0 / ESU R: 1.58
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.4648 --
obs0.4648 207196 99.99 %
Solvent computationSolvent model: NONE
Displacement parametersBiso max: 50 Å2 / Biso mean: 24.734 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0.29 Å2-0.44 Å2
2--1.05 Å2-0.74 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 4.6→95.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7612 0 18 0 7630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01944004
ELECTRON MICROSCOPYr_angle_refined_deg2.1031.95559966
ELECTRON MICROSCOPYr_dihedral_angle_1_deg0.29755457
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.77423.9571893
ELECTRON MICROSCOPYr_dihedral_angle_3_deg2.354156884
ELECTRON MICROSCOPYr_dihedral_angle_4_deg3.17515234
ELECTRON MICROSCOPYr_chiral_restr0.1670.26694
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.02133590
LS refinement shellResolution: 4.6→4.848 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.541 30241 -
obs--100 %

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