7smr

Cryo-EM structure of Torpedo acetylcholine receptor in complex with carbachol, desensitized state

Method: ELECTRON MICROSCOPY Dmax: 149.1 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 × 5 其他Polymer 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–461 Chain D; UniProt 25–461 Not recorded Acetylcholine receptor subunit delta × 1 (P02718) Acetylcholine receptor subunit beta × 1 (P02712) Acetylcholine receptor subunit gamma × 1 (P02714) ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CCE 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM × 2 CLR CHOLESTEROL × 3 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DD9 nonane × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.77 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 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 × 5 其他Polymer 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 22–522 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit beta × 1 (P02712) Acetylcholine receptor subunit gamma × 1 (P02714) ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CCE 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM × 2 CLR CHOLESTEROL × 3 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DD9 nonane × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.77 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 2
Chains and sequence ranges Author chain B; PDBConstruct 1–501; UniProt 22–522

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 × 5 其他Polymer 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 25–493 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit delta × 1 (P02718) Acetylcholine receptor subunit gamma × 1 (P02714) ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CCE 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM × 2 CLR CHOLESTEROL × 3 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DD9 nonane × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.77 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 3
Chains and sequence ranges Author chain C; PDBConstruct 1–469; UniProt 25–493

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 × 5 其他Polymer 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 18–506 Not recorded Acetylcholine receptor subunit alpha × 2 (P02710) Acetylcholine receptor subunit delta × 1 (P02718) Acetylcholine receptor subunit beta × 1 (P02712) ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CCE 2-[(AMINOCARBONYL)OXY]-N,N,N-TRIMETHYLETHANAMINIUM × 2 CLR CHOLESTEROL × 3 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DD9 nonane × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.77 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 7smr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7smr
Deposition date deposition_date2021-10-26
Structure title titleCryo-EM structure of Torpedo acetylcholine receptor in complex with carbachol, desensitized state
Keywords keywords;acetylcholine receptor, nicotinic receptor, Torpedo, Cys-loop receptor, ion channel, muscle-type nicotinic receptor, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.28
Radius of gyration Rg (electron density) rg_electron43.58
Forward intensity I(0) i0730899000.00
Molecular weight molecular_weight241320.0 kDa
Excluded volume excluded_volume309230 ų
Envelope volume envelope_volume395530 ų
Hydration-shell volume shell_volume75876 ų
Envelope diameter envelope_diameter161.0
Shell Rg shell_rg48.57
Envelope Rg envelope_rg43.58
Shape Rg shape_rg43.60
Total Rg total_rg43.76
Total atoms total_atoms17016
Residues n_residues2022
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 dmax149.1
Rg (real space) rg_real44.48
Rg uncertainty (real space) rg_real_error1.11
I(0) (real space) i0_real7.3090e+08
I(0) uncertainty (real space) i0_real_error1.2670e+07
Rg (reciprocal space) rg_reciprocal44.28
I(0) (reciprocal space) i0_reciprocal730700000.0000
Solution quality estimate total_estimate0.8438
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.7
Skewness Skewness skewness0.546
Kurtosis Kurtosis kurtosis-0.089
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha110400000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.714

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id7smrA01
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_id7smrA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id7smrB01
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_id7smrC01
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_id7smrD01
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_id7smrD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id7smrE01
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

8. Citations (1)

9. Files and Curves (10)