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- PDB-9ocl: PV2-10D2 Complex -

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Basic information

Entry
Database: PDB / ID: 9ocl
TitlePV2-10D2 Complex
Components
  • (Capsid protein ...) x 4
  • 10D2 Heavy Chain
  • 10D2 Light Chain
KeywordsVIRUS / Antibody / Complex
Function / homology
Function and homology information


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 / receptor-mediated endocytosis of virus by host cell / 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 / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity ...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 / receptor-mediated endocytosis of virus by host cell / 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 / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus 2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsWaddey, B.T. / Hafenstein, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI10721-01 United States
CitationJournal: Nat Commun / Year: 2026
Title: Neutralizing human monoclonal antibodies to poliovirus map to the receptor binding site.
Authors: Benjamin T Waddey / Andrew J Charnesky / Julia E Faust / Nadia M DiNunno / Rama Devudu Puligedda / Sung Hyun Cho / Carol M Bator / Steven D Dong / Kutub Mahmood / Konstantin M Chumakov / ...Authors: Benjamin T Waddey / Andrew J Charnesky / Julia E Faust / Nadia M DiNunno / Rama Devudu Puligedda / Sung Hyun Cho / Carol M Bator / Steven D Dong / Kutub Mahmood / Konstantin M Chumakov / Scott K Dessain / Susan L Hafenstein /
Abstract: Poliovirus remains a serious threat to human health. Complete eradication of wild-type poliovirus has not yet succeeded, making the development of successful antivirals critical. Microneutralization ...Poliovirus remains a serious threat to human health. Complete eradication of wild-type poliovirus has not yet succeeded, making the development of successful antivirals critical. Microneutralization assays against all three poliovirus serotypes identified a panel of human monoclonal IgGs, which are either serotype-specific or cross-neutralizing. Here, through cryoEM single particle analysis, we solved high resolution structures of four distinct poliovirus-FAb complexes. These antibodies bind to capsids at the circular depression (canyon) surrounding the icosahedral five-fold symmetry axis, which is also the binding site of the poliovirus receptor (PVR). Analysis of these structures confirms overlap of FAb contacts on the viral capsid with those of PVR. For three of the FAbs, the capsid residues are identified that dictate serotype-specific recognition. Contacts for the cross-neutralizing mAb 10D2 are located deep in the capsid canyon. These structural analyses indicate that antibody competition with the receptor likely leads to neutralization of virus particles and inhibition of poliovirus entry into host cells. Thus, the human IgGs studied here may facilitate development of therapeutics for the ongoing efforts in global eradication of poliovirus.
History
DepositionApr 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
H: 10D2 Heavy Chain
L: 10D2 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9067
Polymers122,6496
Non-polymers2561
Water00
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
H: 10D2 Heavy Chain
L: 10D2 Light Chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,374,354420
Polymers7,358,969360
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
H: 10D2 Heavy Chain
L: 10D2 Light Chain
hetero molecules
x 5


  • icosahedral pentamer
  • 615 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)614,53035
Polymers613,24730
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
H: 10D2 Heavy Chain
L: 10D2 Light Chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 737 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)737,43542
Polymers735,89736
Non-polymers1,5396
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
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 / Genome polyprotein


Mass: 33039.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 2 / References: UniProt: P06210
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 29980.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 2 / References: UniProt: P06210
#3: Protein Capsid protein VP3


Mass: 26115.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 2 / References: UniProt: A0A0K1U2R1
#4: Protein Capsid protein VP4


Mass: 7346.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 2 / References: UniProt: D0QXH8

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Antibody , 2 types, 2 molecules HL

#5: Antibody 10D2 Heavy Chain


Mass: 14713.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#6: Antibody 10D2 Light Chain


Mass: 11453.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: PV2-10D2 complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)Organism: Poliovirus 2
Buffer solutionpH: 8
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21_5207model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21606 / Symmetry type: POINT
RefinementHighest resolution: 3.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028491
ELECTRON MICROSCOPYf_angle_d0.49411582
ELECTRON MICROSCOPYf_dihedral_angle_d5.751172
ELECTRON MICROSCOPYf_chiral_restr0.0431286
ELECTRON MICROSCOPYf_plane_restr0.0051494

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