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- PDB-9oco: SIPV3-2E1 Complex -

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Basic information

Entry
Database: PDB / ID: 9oco
TitleSIPV3-2E1 Complex
Components
  • 2E1 Heavy Chain
  • 2E1 Light Chain
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Antibody / Complex
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / 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 / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity ...caveolin-mediated endocytosis of virus by host cell / 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 / 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 speciesPoliovirus 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 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 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
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

Downloads & links

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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
4: VP4
H: 2E1 Heavy Chain
L: 2E1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4047
Polymers123,1486
Non-polymers2561
Water00
1
1: VP1
2: VP2
3: VP3
4: VP4
H: 2E1 Heavy Chain
L: 2E1 Light Chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,404,266420
Polymers7,388,881360
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: VP1
2: VP2
3: VP3
4: VP4
H: 2E1 Heavy Chain
L: 2E1 Light Chain
hetero molecules
x 5


  • icosahedral pentamer
  • 617 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)617,02235
Polymers615,74030
Non-polymers1,2825
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: VP1
2: VP2
3: VP3
4: VP4
H: 2E1 Heavy Chain
L: 2E1 Light Chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 740 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)740,42742
Polymers738,88836
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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Protein , 5 types, 5 molecules 1234H

#1: Protein VP1 / Genome polyprotein


Mass: 33523.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 3 / References: UniProt: P03302
#2: Protein VP2 / Genome polyprotein


Mass: 30169.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 3 / References: UniProt: P03302
#3: Protein VP3 / Genome polyprotein


Mass: 26289.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 3 / References: UniProt: P03302
#4: Protein VP4 / Genome polyprotein


Mass: 7320.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Poliovirus 3 / References: UniProt: P03302
#5: Protein 2E1 Heavy Chain


Mass: 14006.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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

#6: Antibody 2E1 Light Chain


Mass: 11837.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#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: SIPV3-2E1 Complex / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)Organism: Poliovirus 3
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237897 / Symmetry type: POINT
RefinementHighest resolution: 2.95 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038588
ELECTRON MICROSCOPYf_angle_d0.45211695
ELECTRON MICROSCOPYf_dihedral_angle_d5.4981182
ELECTRON MICROSCOPYf_chiral_restr0.0441280
ELECTRON MICROSCOPYf_plane_restr0.0041513

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