7m1h

Crystal structure of LC/A-JPU-C10-JPU-D12-JPU-B8-JPU-G3-ciA-F12-ciA-D12

Method: X-RAY DIFFRACTION

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

Botulinum neurotoxin A light chain

Clostridium botulinum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	JPU-D12 × 1 ciA-F12 × 1 ciA-D12 × 1 JPU-G3 × 1 JPU-C10 × 1 JPU-B8 × 1 ZINC ION × 1 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BXA1_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–445； UniProt 2–438

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	7m1h
Deposition date deposition_date	2021-03-13
Structure title title	Crystal structure of LC/A-JPU-C10-JPU-D12-JPU-B8-JPU-G3-ciA-F12-ciA-D12
Keywords keywords	VHH, protease domain, TOXIN, ANTITOXIN; ANTITOXIN
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.

7m1h__assembly_1__model_1

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

Download this curve (.dat)

7m1h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7m1h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.42 Å
Rg (electron density)	33.53 Å
Total Rg	34.18 Å
Atom count	8868
Residues	1141
Excluded volume	156790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7m1h__assembly_1__model_1`	heptameric （7）	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	Botulinum neurotoxin A light chain
Molecular weight formula_weight	50894.6 kDa
EC 编号 ec_number	3.4.24.69
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	8918

GPLGSPEFPFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEFYKLLCVRGIITSK

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	JPU-D12
Molecular weight formula_weight	13747.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSQLQLVESGGGTVQPGGTLRLSCAASGFTLDEYAIGWFRQAPGKEREGVSCISSSASISYADSVKGRFTISRDNAKNTVYLTMNSLKPEDTGVYYCARAFLACGPVAGWGTEYDYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ciA-F12
Molecular weight formula_weight	14109.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLGSQVQLVESGGGLVQPGGSLRLSCAASGFTLGSRYMSWVRQAPGEGFEWVSSIEPSGTAWDGDSAKGRFTTSRDDAKNTLYLQMSNLQPEDTGVYYCATGYRTDTRIPGGSWGQGTQVTVSSEPKTPKPQ

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	ciA-D12
Molecular weight formula_weight	14404.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GSQVQLVESGGGLVQPGGSLRLSCVVSGSDFNTYIMGWYRQVPGKPRELVADITTEGKTNYGGSVKGRFTISRDNAKNTVYLQMFGLKPEDAGNYVCNADWKMGAWTAGDYGIDYWGKGTLVTVSSGPKTPKPQ

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	JPU-G3
Molecular weight formula_weight	13698.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPLGSQVQLAETGGGLVQPGGSLRLSCTASTTISDFYSMGWFRQTPGNQRELVAIVRRGGDTKSGDSVKGRFTISRDNTRSTVYLQMDNLKPEDTAVYYCYANLQKSSDELGPYYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	JPU-C10
Molecular weight formula_weight	13810.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

GPLGSQLQLVESGGGLVQPGGSLRLSCAASGNIFSIYYMGWYRQAPGKQREMVAIINSNGITNYGDFVKGRFTISRDNAENSAYLQMNNLTPEDTAVYYCNAGKLRRTTGWGLDDYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	JPU-B8
Molecular weight formula_weight	13329.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GPLGSQVQLVESGGGLVQPGGSLRLSCAASGSIFSIYAMGWYRQAPGKQRELVAAISSYGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNADIATMTAVGGFDYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	7m1hB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7m1hC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7m1hD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7m1hF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7m1hG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	77.590 Å
Unit-cell length b length_b	93.983 Å
Unit-cell length c length_c	231.748 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	115.870 Å
R factor r_factor	0.2184
R_work r_work	0.2168
R_free r_free	0.2488

Crystal structure of LC/A-JPU-C10-JPU-D12-JPU-B8-JPU-G3-ciA-F12-ciA-D12

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

Botulinum neurotoxin A light chain

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

7m1h__assembly_1__model_1

7m1h__assembly_1__model_1 | I(q)

7m1h__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 (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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)