9OEA | pdb_00009oea

SIPV1-5E12 Complex

• PDB DOI: https://doi.org/10.2210/pdb9OEA/pdb
• EM Map EMD-70392: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Human poliovirus 1 strain Sabin, Homo sapiens
• Mutation(s): No 


• Deposited: 2025-04-28 Released: 2025-12-17 
• Deposition Author(s): Waddey, B.T., Hafenstein, S.L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Neutralizing human monoclonal antibodies to poliovirus map to the receptor binding site

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.

(2025) Nat Commun 

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A60B60C60D60E60F60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 360-mer - A120B60C60D60E60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 123.74 kDa 
• Atom Count: 8,347 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,114 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth 1]	302	Human poliovirus 1 strain Sabin	Mutation(s): 0
UniProt
Find proteins for P03301 (Poliovirus type 1 (strain Sabin)) Explore P03301  Go to UniProtKB:  P03301

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B [auth 2]	272	Human poliovirus 1 strain Sabin	Mutation(s): 0
UniProt
Find proteins for P03301 (Poliovirus type 1 (strain Sabin)) Explore P03301  Go to UniProtKB:  P03301

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C [auth 3]	238	Human poliovirus 1 strain Sabin	Mutation(s): 0
UniProt
Find proteins for P03301 (Poliovirus type 1 (strain Sabin)) Explore P03301  Go to UniProtKB:  P03301

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D [auth 4]	68	Human poliovirus 1 strain Sabin	Mutation(s): 0
UniProt
Find proteins for P03301 (Poliovirus type 1 (strain Sabin)) Explore P03301  Go to UniProtKB:  P03301

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
5E12 Heavy Chain	E [auth H]	127	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
5E12 Light Chain	F [auth L]	107	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM (Subject of Investigation/LOI)	G [auth 1]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	cryoSPARC	4.6.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Waddey, B.T., Hafenstein, S.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI10721-01

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release