9ML3 | pdb_00009ml3

B25M05 Fab bound to HPV16 L1 pentamer

• PDB DOI: https://doi.org/10.2210/pdb9ML3/pdb
• EM Map EMD-48346: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Human papillomavirus 16, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-12-18 Released: 2025-08-20 
• Deposition Author(s): Hurlburt, N.K., Singh, S., Rodarte, J.V., Pancera, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

HPV16 neutralizing monoclonal antibodies show evidence for common developmental pathways and public epitopes

Carter, J.J., Hurlburt, N.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A5B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A5B2 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 286.44 kDa 
• Atom Count: 18,069 
• Modeled Residue Count: 2,292 
• Deposited Residue Count: 2,584 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein L1	A, B, C, D, E	426	Human papillomavirus 16	Mutation(s): 0  Gene Names: L1
UniProt
Find proteins for A0A451ER69 (Human papillomavirus type 16) Explore A0A451ER69  Go to UniProtKB:  A0A451ER69

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B25M05 Fab Heavy Chain	F [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B25M05 Fab Light Chain	G [auth L]	216	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Hurlburt, N.K., Singh, S., Rodarte, J.V., Pancera, M.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release