7z14

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with a short-chain neurotoxin.

Method: ELECTRON MICROSCOPY Dmax: 132.5 Å Quality: GOOD

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

Acetylcholine receptor subunit alpha

OrganismNot specified

UniProt P02710

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 7 其他Polymer 5 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 25–461 Chain D; UniProt 25–461 Not recorded Acetylcholine receptor subunit beta × 1 (P02712) Acetylcholine receptor subunit delta × 1 (P02718) Acetylcholine receptor subunit gamma × 1 (P02714) Consensus short-chain short-chain alpha-neurotoxin ScNtx × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHA_TETCF
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–437; UniProt 25–461 Author chain D; PDBConstruct 1–437; UniProt 25–461

Acetylcholine receptor subunit beta

OrganismNot specified

UniProt P02712

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 7 其他Polymer 5 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 25–493 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit delta × 1 (P02718) Acetylcholine receptor subunit gamma × 1 (P02714) Consensus short-chain short-chain alpha-neurotoxin ScNtx × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHB_TETCF
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–469; UniProt 25–493

Acetylcholine receptor subunit delta

OrganismNot specified

UniProt P02718

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 7 其他Polymer 5 PDB declaration: heptameric(7) Consistent with protein copy count Chain C; UniProt 22–522 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit beta × 1 (P02712) Acetylcholine receptor subunit gamma × 1 (P02714) Consensus short-chain short-chain alpha-neurotoxin ScNtx × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHD_TETCF
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–501; UniProt 22–522

Acetylcholine receptor subunit gamma

OrganismNot specified

UniProt P02714

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 7 其他Polymer 5 PDB declaration: heptameric(7) Consistent with protein copy count Chain E; UniProt 18–506 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit beta × 1 (P02712) Acetylcholine receptor subunit delta × 1 (P02718) Consensus short-chain short-chain alpha-neurotoxin ScNtx × 2 ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.15 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.

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACHG_TETCF
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–489; UniProt 18–506

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 7z14

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7z14
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7z14
Deposition date deposition_date2022-02-24
Structure title titleCryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with a short-chain neurotoxin.
Keywords keywordsIon channel, toxin, membrane protein; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.66
Radius of gyration Rg (electron density) rg_electron39.85
Forward intensity I(0) i0661871000.00
Molecular weight molecular_weight225060.0 kDa
Excluded volume excluded_volume287140 ų
Envelope volume envelope_volume367890 ų
Hydration-shell volume shell_volume74586 ų
Envelope diameter envelope_diameter130.8
Shell Rg shell_rg47.39
Envelope Rg envelope_rg39.61
Shape Rg shape_rg39.83
Total Rg total_rg40.31
Total atoms total_atoms15856
Residues n_residues1913
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax132.5
Rg (real space) rg_real40.54
Rg uncertainty (real space) rg_real_error1.33
I(0) (real space) i0_real6.6190e+08
I(0) uncertainty (real space) i0_real_error1.2060e+07
Rg (reciprocal space) rg_reciprocal40.66
I(0) (reciprocal space) i0_reciprocal662000000.0000
Solution quality estimate total_estimate0.8868
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.0
Skewness Skewness skewness0.247
Kurtosis Kurtosis kurtosis-0.381
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha87400000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id7z14A01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id7z14B01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id7z14C01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id7z14D01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id7z14E01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id7z14F01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology60 — CD59
Homologous superfamily homologous superfamily10 — CD59

8. Citations (1)

9. Files and Curves (10)