9CK4 | pdb_00009ck4

L9 epitope scaffold complexed with L9 Fabs

• PDB DOI: https://doi.org/10.2210/pdb9CK4/pdb
• EM Map EMD-45640: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Plasmodium falciparum 3D7, Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2024-07-08 Released: 2026-01-21 
• Deposition Author(s): Raghavan, S.S.R., Lee, W.H., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Scaffolding disordered repeat epitopes of Plasmodium falciparum circumsporozoite by combined machine learning approaches

Raghavan, S.S.R., Lee, W.H., Ward, A.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B3C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 86.75 kDa 
• Atom Count: 5,942 
• Modeled Residue Count: 758 
• Deposited Residue Count: 777 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L9 epitope Scaffold	A [auth W]	99	Plasmodium falciparum 3D7	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L9 heavy chain	B [auth A], D [auth E], F [auth C]	119	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
L9 light chain	C [auth B], E [auth F], G [auth D]	107	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Raghavan, S.S.R., Lee, W.H., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release