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9e3j

Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171

Method: ELECTRON MICROSCOPY Dmax: 108.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pertussis toxin subunit 1

Bordetella pertussis

UniProt T1SR96

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 × 8 PDB declaration: octameric（8） 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-171 HC × 1 PERT-171 LC × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 9E3J 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 oligomeric state 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
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
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
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 3.40 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 × 8 PDB declaration: octameric（8） 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-171 HC × 1 PERT-171 LC × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 9E3J 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 oligomeric state 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
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
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
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 3.40 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 × 8 PDB declaration: octameric（8） 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-171 HC × 1 PERT-171 LC × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 9E3J 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
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
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
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 3.40 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07 Different construct Different oligomeric state 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 × 8 PDB declaration: octameric（8） 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-171 HC × 1 PERT-171 LC × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 9E3J 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
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
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
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 3.40 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07 Different construct Different oligomeric state 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 × 8 PDB declaration: octameric（8） 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-171 HC × 1 PERT-171 LC × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.60 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 9E3J 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
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
9E3L Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203 Deposited 2024-10-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
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 3.40 Å
9MR7 Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab Deposited 2025-01-07 Different construct Different oligomeric state 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

SAXS profile for 9e3j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9e3j
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9e3j
Deposition date deposition_date2024-10-23
Structure title titleCryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-171
Keywords keywordsPTx, mAb, Whooping, TOXIN, TOXIN-Immune System complex; TOXIN/Immune System
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.69 Å
Radius of gyration Rg (electron density) rg_electron31.88 Å
Forward intensity I(0) i0214508000.00
Molecular weight molecular_weight115560.0 kDa
Excluded volume excluded_volume143810 ų
Envelope volume envelope_volume179900 ų
Hydration-shell volume shell_volume46657 ų
Envelope diameter envelope_diameter115.7 Å
Shell Rg shell_rg39.12 Å
Envelope Rg envelope_rg31.99 Å
Shape Rg shape_rg31.91 Å
Total Rg total_rg32.34 Å
Total atoms total_atoms8113
Residues n_residues1038
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax108.6 Å
Rg (real space) rg_real32.64 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real2.1450e+08
I(0) uncertainty (real space) i0_real_error3.1760e+06
Rg (reciprocal space) rg_reciprocal32.67 Å
I(0) (reciprocal space) i0_reciprocal214500000.0000
Solution quality estimate total_estimate0.8845
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.7 Å
Skewness Skewness skewness0.338
Kurtosis Kurtosis kurtosis-0.269
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51930000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.966
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)