8E8X

9H2 Fab-Sabin poliovirus 3 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A human monoclonal antibody binds within the poliovirus receptor-binding site to neutralize all three serotypes.

Charnesky, A.J.Faust, J.E.Lee, H.Puligedda, R.D.Goetschius, D.J.DiNunno, N.M.Thapa, V.Bator, C.M.Cho, S.H.J.Wahid, R.Mahmood, K.Dessain, S.Chumakov, K.M.Rosenfeld, A.Hafenstein, S.L.

(2023) Nat Commun 14: 6335-6335

  • DOI: https://doi.org/10.1038/s41467-023-41052-9
  • Primary Citation of Related Structures:  
    8E8L, 8E8R, 8E8S, 8E8X, 8E8Y, 8E8Z

  • PubMed Abstract: 

    Global eradication of poliovirus remains elusive, and it is critical to develop next generation vaccines and antivirals. In support of this goal, we map the epitope of human monoclonal antibody 9H2 which is able to neutralize the three serotypes of poliovirus. Using cryo-EM we solve the near-atomic structures of 9H2 fragments (Fab) bound to capsids of poliovirus serotypes 1, 2, and 3. The Fab-virus complexes show that Fab interacts with the same binding mode for each serotype and at the same angle of interaction relative to the capsid surface. For each of the Fab-virus complexes, we find that the binding site overlaps with the poliovirus receptor (PVR) binding site and maps across and into a depression in the capsid called the canyon. No conformational changes to the capsid are induced by Fab binding for any complex. Competition binding experiments between 9H2 and PVR reveal that 9H2 impedes receptor binding. Thus, 9H2 outcompetes the receptor to neutralize poliovirus. The ability to neutralize all three serotypes, coupled with the critical importance of the conserved receptor binding site make 9H2 an attractive antiviral candidate for future development.


  • Organizational Affiliation

    Molecular, Cellular, and Integrative Biosciences Program, The Pennsylvania State University, University Park, PA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1A [auth 1]279Human poliovirus 3 strain SabinMutation(s): 0 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
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UniProt GroupP03302
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2B [auth 2]263Human poliovirus 3 strain SabinMutation(s): 0 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03302
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3C [auth 3]235Human poliovirus 3 strain SabinMutation(s): 0 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
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UniProt GroupP03302
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP4D [auth 4]68Human poliovirus 3 strain SabinMutation(s): 0 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
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UniProt GroupP03302
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
9H2 Fab heavy chainE [auth H]126Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
9H2 Fab light chainF [auth L]110Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
G [auth 1]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesOD026822-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI107121-01
Bill & Melinda Gates FoundationUnited StatesOPP1135787

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references