9e3l

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203

Method: ELECTRON MICROSCOPY D_max: 138.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pertussis toxin subunit 1

Bordetella pertussis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain A； UniProt 1–269	Not recorded	Islet-activating protein S2 × 1 （A0A0E8DFW5） Pertussis toxin subunit 3 × 1 （P04979） Pertussis toxin subunit 4 × 2 （P0A3R5） Pertussis toxin subunit 5 × 1 （P04981） PERT-203 HC × 1 PERT-203 LC × 1 PERT-169 HC × 2 PERT-169 LC × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9E3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6RO0 CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT. Deposited 2019-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–269（269 aa） Chain G 1–269（269 aa）	Mutation：R9K, E129G Mutation：R9K, E129G	GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–269（269 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	T1SR96_BORPT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–269； UniProt 1–269

Islet-activating protein S2

Bordetella pertussis

UniProt A0A0E8DFW5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain B； UniProt 1–226	Not recorded	Pertussis toxin subunit 1 × 1 （T1SR96） Pertussis toxin subunit 3 × 1 （P04979） Pertussis toxin subunit 4 × 2 （P0A3R5） Pertussis toxin subunit 5 × 1 （P04981） PERT-203 HC × 1 PERT-203 LC × 1 PERT-169 HC × 2 PERT-169 LC × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9E3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6RO0 CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT. Deposited 2019-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–226（226 aa） Chain H 1–226（226 aa）	Not recorded	GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；278 K；Spontaneous crystallization in plastic bottles	Resolution 2.13 Å R-free 0.260
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain B 1–226（226 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0E8DFW5_BORPT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–226； UniProt 1–226

Pertussis toxin subunit 3

Bordetella pertussis

UniProt P04979

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain C； UniProt 1–227	Not recorded	Pertussis toxin subunit 1 × 1 （T1SR96） Islet-activating protein S2 × 1 （A0A0E8DFW5） Pertussis toxin subunit 4 × 2 （P0A3R5） Pertussis toxin subunit 5 × 1 （P04981） PERT-203 HC × 1 PERT-203 LC × 1 PERT-169 HC × 2 PERT-169 LC × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9E3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 29–227（199 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 29–227（199 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–227（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 32–227（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PTO THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING Deposited 1994-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 32–227（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å
1PTO THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING Deposited 1994-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 32–227（196 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C 1–227（227 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–227（227 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain C 1–227（227 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 29–227（199 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOX3_BORPE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–227； UniProt 1–227

Pertussis toxin subunit 4

Bordetella pertussis

UniProt P0A3R5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain D； UniProt 1–152 Chain E； UniProt 1–152	Not recorded	Pertussis toxin subunit 1 × 1 （T1SR96） Islet-activating protein S2 × 1 （A0A0E8DFW5） Pertussis toxin subunit 3 × 1 （P04979） Pertussis toxin subunit 5 × 1 （P04981） PERT-203 HC × 1 PERT-203 LC × 1 PERT-169 HC × 2 PERT-169 LC × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9E3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 43–152（110 aa） Chain E 43–152（110 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 43–152（110 aa） Chain K 43–152（110 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 43–152（110 aa） Chain E 43–152（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 43–152（110 aa） Chain K 43–152（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 1–152（152 aa） Chain E 1–152（152 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–152（152 aa） Chain E 1–152（152 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 1–152（152 aa） Chain E 1–152（152 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 43–152（110 aa） Chain E 43–152（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOX4_BORPE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–152； UniProt 1–152 Author chain E； PDBConstruct 1–152； UniProt 1–152

Pertussis toxin subunit 5

Bordetella pertussis

UniProt P04981

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain F； UniProt 1–133	Not recorded	Pertussis toxin subunit 1 × 1 （T1SR96） Islet-activating protein S2 × 1 （A0A0E8DFW5） Pertussis toxin subunit 3 × 1 （P04979） Pertussis toxin subunit 4 × 2 （P0A3R5） PERT-203 HC × 1 PERT-203 LC × 1 PERT-169 HC × 2 PERT-169 LC × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9E3L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 35–133（99 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1BCP BINARY COMPLEX OF PERTUSSIS TOXIN AND ATP Deposited 1995-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 35–133（99 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.70 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 36–133（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PRT THE CRYSTAL STRUCTURE OF PERTUSSIS TOXIN Deposited 1993-11-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 36–133（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1PTO THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING Deposited 1994-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 36–133（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å
1PTO THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING Deposited 1994-03-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 36–133（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å
9E3H Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-61 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain F 1–133（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E3J Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–133（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9E3K Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199 Deposited 2024-10-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain F 1–133（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 35–133（99 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOX5_BORPE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–133； UniProt 1–133

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9e3l
Deposition date deposition_date	2024-10-23
Structure title title	Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203
Keywords keywords	PTx, mAb, Whooping, TOXIN, TOXIN-Immune System complex; TOXIN/Immune System
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.99 Å
Radius of gyration Rg (electron density) rg_electron	40.91 Å
Forward intensity I(0) i0	440405000.00
Molecular weight molecular_weight	169670.0 kDa
Excluded volume excluded_volume	211590 Å³
Envelope volume envelope_volume	284400 Å³
Hydration-shell volume shell_volume	59977 Å³
Envelope diameter envelope_diameter	143.7 Å
Shell Rg shell_rg	44.14 Å
Envelope Rg envelope_rg	40.82 Å
Shape Rg shape_rg	40.92 Å
Total Rg total_rg	41.04 Å
Total atoms total_atoms	11931
Residues n_residues	1548
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	138.9 Å
Rg (real space) rg_real	40.99 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	4.4040e+08
I(0) uncertainty (real space) i0_real_error	7.3310e+06
Rg (reciprocal space) rg_reciprocal	40.99 Å
I(0) (reciprocal space) i0_reciprocal	440400000.0000
Solution quality estimate total_estimate	0.8870
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	38370000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.937

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Pertussis toxin subunit 1
Molecular weight formula_weight	30005.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11931

MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSSNSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQAESSEAMAAWSERAGEAMVLVYYESIAYSF

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 2 Entity 2 polymer

Description description	Islet-activating protein S2
Molecular weight formula_weight	24856.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 3 Entity 3 polymer

Description description	Pertussis toxin subunit 3
Molecular weight formula_weight	25012.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGWSIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIGACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 4 Entity 4 polymer

Description description	Pertussis toxin subunit 4
Molecular weight formula_weight	16566.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 5 Entity 5 polymer

Description description	Pertussis toxin subunit 5
Molecular weight formula_weight	14513.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE

来源 Source

来源生物 organism	Bordetella pertussis
NCBI Class编号 ncbi_taxonomy_id	520
宿主生物 host_organism	Bordetella pertussis

Entity 6 Entity 6 polymer

Description description	PERT-203 HC
Molecular weight formula_weight	24581.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

QVQLQESGPGLVKPSGTLSLTCAVSGGSISSNDWWSWVRQSPGKGLEWIGESYHSGGTNYNPSLTSRVTISVDQSKNHFSLRLSSVTAADTAVYFCARRTIGNYDISTGYYTPAVFFDSWGQGILVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	PERT-203 LC
Molecular weight formula_weight	24143.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNTYNYLDWYLQKPGQSPQLLIYLGSHRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQSLQTPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 8 Entity 8 polymer

Description description	PERT-169 HC
Molecular weight formula_weight	24570.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K

QVQLVQAGGEVKKPGTSVNVSCKASVYTFTNYYLHWVRQAPGQGLEWMGVMNPSGGKTIYAQKFQGRVTTTRDTSTSTVYMELRSLRSEDTAVYYCARGLYYGDSSGYFGAGEFDHWGQGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 9 Entity 9 polymer

Description description	PERT-169 LC
Molecular weight formula_weight	22848.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L

QAVVTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPFWLQQKPGQAPRTLIYDTSNKHSWTPARFSASLLGGKAALTLSGAQPEDEAEYYCLLSYSGARRVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	123270

fit	/app/data/saxs_computation/e3/9e3l/9e3l.fit
pddf	/app/data/pr_computation/e3/9e3l/9e3l.pr.out
profile	/app/data/saxs_computation/e3/9e3l/9e3l.dat

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203

1. Protein Identity and Related Structures Protein Identity & Related Structures

Pertussis toxin subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Islet-activating protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Pertussis toxin subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Pertussis toxin subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Pertussis toxin subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

Entity 8 Entity 8 polymer

Polymer Polymer

来源 Source

Entity 9 Entity 9 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)