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- PDB-9oea: SIPV1-5E12 Complex -

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Basic information

Entry
Database: PDB / ID: 9oea
TitleSIPV1-5E12 Complex
Components
  • (Capsid protein ...) x 4
  • 5E12 Heavy Chain
  • 5E12 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / 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
Similarity search - Component
Biological speciesHuman poliovirus 1 strain Sabin
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 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: 2025
Title: Neutralizing human monoclonal antibodies to poliovirus map to the receptor binding site
Authors: Waddey, B.T. / Charnesky, A.J. / Faust, J.E. / DiNunno, N.M. / Cho, S.H. / Bator, C.M. / Dong, S. / Mahmood, K. / Chumakov, K.M. / Dessain, S.K. / Hafenstein, S.L.
History
DepositionApr 28, 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
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
H: 5E12 Heavy Chain
L: 5E12 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7447
Polymers123,4886
Non-polymers2561
Water00
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
H: 5E12 Heavy Chain
L: 5E12 Light Chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,424,657420
Polymers7,409,271360
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: 5E12 Heavy Chain
L: 5E12 Light Chain
hetero molecules
x 5


  • icosahedral pentamer
  • 619 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)618,72135
Polymers617,43930
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: 5E12 Heavy Chain
L: 5E12 Light Chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 742 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)742,46642
Polymers740,92736
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


Mass: 33492.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 strain Sabin / References: UniProt: P03301
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 30110.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 strain Sabin / References: UniProt: P03301
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26593.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 strain Sabin / References: UniProt: P03301
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 7409.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 strain Sabin / References: UniProt: P03301

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Antibody , 2 types, 2 molecules HL

#5: Antibody 5E12 Heavy Chain


Mass: 14329.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#6: Antibody 5E12 Light Chain


Mass: 11552.662 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: SIPV1-5E12 FAb complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 1 strain Sabin
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
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26641 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028560
ELECTRON MICROSCOPYf_angle_d0.46811656
ELECTRON MICROSCOPYf_dihedral_angle_d5.3251173
ELECTRON MICROSCOPYf_chiral_restr0.0431290
ELECTRON MICROSCOPYf_plane_restr0.0041507

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