9E3K | pdb_00009e3k

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199

• PDB DOI: https://doi.org/10.2210/pdb9E3K/pdb
• EM Map EMD-47486: EMDB EMDataResource

• Classification: TOXIN/Immune System
• Organism(s): Bordetella pertussis, Homo sapiens
• Expression System: Bordetella pertussis, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-23 Released: 2025-10-29 
• Deposition Author(s): Binshtein, E., Crowe, J.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199

Binshtein, E., Crowe, J.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B4C1D1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 178.78 kDa 
• Atom Count: 10,021 
• Modeled Residue Count: 1,300 
• Deposited Residue Count: 1,635 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertussis toxin subunit 1	A	269	Bordetella pertussis	Mutation(s): 0  Gene Names: ptxA
UniProt
Find proteins for T1SR96 (Bordetella pertussis) Explore T1SR96  Go to UniProtKB:  T1SR96

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Islet-activating protein S2	B	226	Bordetella pertussis	Mutation(s): 0  Gene Names: ptxB, NCTC10911_00247
UniProt
Find proteins for A0A0E8DFW5 (Bordetella pertussis) Explore A0A0E8DFW5  Go to UniProtKB:  A0A0E8DFW5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertussis toxin subunit 3	C	227	Bordetella pertussis	Mutation(s): 0  Gene Names: ptxC, BP3787
UniProt
Find proteins for P04979 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore P04979  Go to UniProtKB:  P04979

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertussis toxin subunit 4	D, E	152	Bordetella pertussis	Mutation(s): 0  Gene Names: ptxD, BP3785
UniProt
Find proteins for P0A3R5 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore P0A3R5  Go to UniProtKB:  P0A3R5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Pertussis toxin subunit 5	F	133	Bordetella pertussis	Mutation(s): 0  Gene Names: ptxE, BP3786
UniProt
Find proteins for P04981 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore P04981  Go to UniProtKB:  P04981

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PERT-199 HC	G [auth H], J	130	Homo sapiens	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PERT-199 LC	H [auth K], I [auth L]	108	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 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: 2025-10-29 
Deposition Author(s): Binshtein, E., Crowe, J.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release