7l6v

Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12

Method: X-RAY DIFFRACTION

▼

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

BoNT/A

Clostridium botulinum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	JPU-C1 × 1 JPU-A5 × 1 JPU-H7 × 1 Single-domain antibody VHH ciA-F12 × 1 JPU-D12 × 1 1,2-ETHANEDIOL × 2 ZINC ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7B8V4_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–425； UniProt 1–420

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7l6v
Deposition date deposition_date	2020-12-24
Structure title title	Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12
Keywords keywords	neurotoxin, enzyme inhibitor, ANTITOXIN; ANTITOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

7l6v__assembly_1__model_1

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

Download this curve (.dat)

7l6v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7l6v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.19 Å
Rg (electron density)	32.31 Å
Total Rg	32.93 Å
Atom count	7974
Residues	1029
Excluded volume	140760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7l6v__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	BoNT/A
Molecular weight formula_weight	48551.8 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	8494

GPLGSMPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFT

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-C1
Molecular weight formula_weight	13297.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSQVQLAESGGGLVQPGGSLRLSCAASGFTFNRYVIRWYRQAPGKERELVAGISRSGDSGRYVDSVKGRFTISRDNDKNMAYLQMSSLKPDDTAVYYCSALNLEDMEYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	JPU-A5
Molecular weight formula_weight	13674.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLGSQVQLVETGGGLVQAGGSLRLSCTASGADFSFYAMGWYRQTPGNSRELVAVMNLNGVISYGDSARGRFDISRDGTKNIVFLQMNSLKPEDTGVYYCNGMRLYTRGSVRHPESWGQGIQVTVSS

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	JPU-H7
Molecular weight formula_weight	13326.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPLGSQVQLVESGGGSVQPGGSLRLSCAAIGSVFTMYTTAWYRQTPGNLRELVASITDEHRTNYAASAEGRFTISRDNAKHTVDLQMTNLKPEDTAVYYCKLEHDLGYYDYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Single-domain antibody VHH ciA-F12
Molecular weight formula_weight	13201.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

GPLGSQVQLVESGGGLVQPGGSLRLSCAASGFTLGSRYMSWVRQAPGEGFEWVSSIEPSGTAWDGDSAKGRFTTSRDDAKNTLYLQMSNLQPEDTGVYYCATGYRTDTRIPGGSWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 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	F

GPLGSQLQLVESGGGTVQPGGTLRLSCAASGFTLDEYAIGWFRQAPGKEREGVSCISSSASISYADSVKGRFTISRDNAKNTVYLTMNSLKPEDTGVYYCARAFLACGPVAGWGTEYDYWGQGTQVTVSS

Source Source

Source organism organism	Vicugna pacos
Common name common_name	alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	520

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7l6vB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7l6vD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7l6vE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7l6vF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	115.899 Å
Unit-cell length b length_b	157.645 Å
Unit-cell length c length_c	173.001 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	116.520 Å
R factor r_factor	0.1986
R_work r_work	0.1968
R_free r_free	0.2344

Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12

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

BoNT/A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7l6v__assembly_1__model_1

7l6v__assembly_1__model_1 | I(q)

7l6v__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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of BoNT/A-LC-JPU-A5-JPU-C1-JPU-H7-JPU-D12-ciA-F12

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

BoNT/A

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

7l6v__assembly_1__model_1

7l6v__assembly_1__model_1 | I(q)

7l6v__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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)