9e3l

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

Method: ELECTRON MICROSCOPY

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	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	Consistent with protein count

Other States of the Same Protein in the Database

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9e3l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9e3l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e3l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.99 Å
Rg (electron density)	40.91 Å
Total Rg	41.04 Å
Atom count	11931
Residues	1548
Excluded volume	211590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e3l__assembly_1__model_1`	12-meric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism 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

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism 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

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism 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

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism 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

Source Source

Source organism organism	Bordetella pertussis
NCBI taxonomy ID ncbi_taxonomy_id	520
Host organism 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

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

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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Method resolution_method	—
颗粒数 num_particles	123270

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Islet-activating protein S2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pertussis toxin subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pertussis toxin subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pertussis toxin subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9e3l__assembly_1__model_1

9e3l__assembly_1__model_1 | I(q)

9e3l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

7. Citations (1)