4qd2

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex

Method: X-RAY DIFFRACTION

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

Hemagglutinin component HA33

Clostridium botulinum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA17 × 1 （A5HZZ5） Hemagglutinin component HA70 × 1 （A5HZZ4） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA17 × 1 （A5HZZ5） Hemagglutinin component HA70 × 1 （A5HZZ4） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5HZZ6_CLOBH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–292； UniProt 2–293 Author chain D； PDBConstruct 1–292； UniProt 2–293 Author chain H； PDBConstruct 1–292； UniProt 2–293 Author chain I； PDBConstruct 1–292； UniProt 2–293

Hemagglutinin component HA17

Clostridium botulinum

UniProt A5HZZ5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA70 × 1 （A5HZZ4） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA70 × 1 （A5HZZ4） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5HZZ5_CLOBH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–147； UniProt 2–146 Author chain G； PDBConstruct 3–147； UniProt 2–146

Hemagglutinin component HA70

Clostridium botulinum

UniProt A5HZZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA17 × 1 （A5HZZ5） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA17 × 1 （A5HZZ5） Cadherin-1 × 1 （P09803） CALCIUM ION × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5HZZ4_CLOBH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 6–254； UniProt 378–626 Author chain F； PDBConstruct 6–254； UniProt 378–626

Cadherin-1

Mus musculus

UniProt P09803

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA17 × 1 （A5HZZ5） Hemagglutinin component HA70 × 1 （A5HZZ4） CALCIUM ION × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Hemagglutinin component HA33 × 2 （A5HZZ6） Hemagglutinin component HA17 × 1 （A5HZZ5） Hemagglutinin component HA70 × 1 （A5HZZ4） CALCIUM ION × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CADH1_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–213； UniProt 157–369 Author chain J； PDBConstruct 1–213； UniProt 157–369

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	4qd2
Deposition date deposition_date	2014-05-13
Structure title title	Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex
Keywords keywords	Oral Toxicity, Botulinum Neurotoxin, E-Cadherin, HA70, HA17, HA33, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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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.

4qd2__assembly_1__model_1

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

Download this curve (.dat)

4qd2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qd2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.31 Å
Rg (electron density)	38.86 Å
Total Rg	39.04 Å
Atom count	9301
Residues	1151
Excluded volume	164570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qd2__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qd2__assembly_2__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin component HA33
Molecular weight formula_weight	34081.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C,I,H
Atom count atom_count	19012

EHYSVIQNSLNDKIVTISCKADTNLFFYQVAGNVSLFQQTRNYLERWRLIYDSNKAAYKIKSMDIHNTNLVLTWNAPTHNISTQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYADTVARNLKLSTLNNSNYIKFIIEDYIISDLNNFTCKISPILDLNKVVQQVDVTNLNVNLYTWDYGRNQKWTIRYNEEKAAYQFFNTILSNGVLTWIFSNGNTVRVSSSNDQNNDAQYWLINPVSDTDETYTITNLRDTTKALDLYGGQTANGTAIQVFNYHGDDNQKWNIRNPPGSA

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	441771
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Hemagglutinin component HA17
Molecular weight formula_weight	17069.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,G

GPSVERTFLPNGNYNIKSIFSGSLYLNPVSKSLTFSNESSANNQKWNVEYMAENRCFKISNVAEPNKYLSYDNFGFISLDSLSNRCYWFPIKIAVNTYIMLSLNKVNELDYAWDIYDTNENILSQPLLLLPNFDIYNSNQMFKLEKI

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	441771
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Hemagglutinin component HA70
Molecular weight formula_weight	28846.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F

GPLGSPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIYEAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIENQIQFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDTSNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLHLLNNTNSIRLLNGAIYILKVEVTELNNYNIRLHIDITN

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	441771
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cadherin-1
Molecular weight formula_weight	23260.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DWVIPPISCPENEKGEFPKNLVQIKSNRDKETKVFYSITGQGADKPPVGVFIIERETGWLKVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAEGAVPGTSVMKVSATDADDDVNTYNAAIAYTIVSQDPELPHKNMFTVNRDTGVISVLTSGLDRESYPTYTLVVQAADLQGEGLSTTAKAVITVKD

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	402

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6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d4qd2c1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4qd2d1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2d2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2d3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4qd2e1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d4qd2e2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d4qd2h1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2h2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2h3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4qd2i1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2i2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d4qd2i3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4qd2j1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d4qd2j2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

CATH v4.4 (16 domains)

Domain ID domain_id	4qd2A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1090 —

Domain ID domain_id	4qd2B00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2C01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2C02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2D01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2D02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	4qd2E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	4qd2F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1090 —

Domain ID domain_id	4qd2G00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2H01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2H02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2I01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2I02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4qd2J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	4qd2J02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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Unit-cell length a length_a	86.990 Å
Unit-cell length b length_b	95.730 Å
Unit-cell length c length_c	96.140 Å
Unit-cell angle α angle_alpha	116.89 °
Unit-cell angle β angle_beta	96.34 °
Unit-cell angle γ angle_gamma	93.70 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	47.730 Å
R factor r_factor	0.2100
R_work r_work	0.2080
R_free r_free	0.2470

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex

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

Hemagglutinin component HA33

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin component HA17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin component HA70

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cadherin-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4qd2__assembly_1__model_1

4qd2__assembly_1__model_1 | I(q)

4qd2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 31 domains

SCOP 2.08 (15 domains)

CATH v4.4 (16 domains)

7. Citations (1)