8f6y

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate, desensitized-like state

Method: ELECTRON MICROSCOPY

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

Acetylcholine receptor subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 5	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 Etomidate × 2 CHOLINE ION × 2 CHOLESTEROL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 nonane × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACHA_TETCF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–433； UniProt 25–457 Author chain D； PDBConstruct 1–433； UniProt 25–457

Acetylcholine receptor subunit delta

OrganismNot specified

UniProt P02718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 5	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 Etomidate × 2 CHOLINE ION × 2 CHOLESTEROL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 nonane × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACHD_TETCF
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–500； UniProt 22–521

Acetylcholine receptor subunit beta

OrganismNot specified

UniProt P02712

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 5	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 Etomidate × 2 CHOLINE ION × 2 CHOLESTEROL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 nonane × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 5	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 Etomidate × 2 CHOLINE ION × 2 CHOLESTEROL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6 nonane × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8f6y
Deposition date deposition_date	2022-11-17
Structure title title	Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate, desensitized-like state
Keywords keywords	;acetylcholine receptor, nicotinic receptor, Torpedo, Cys-loop receptor, ion channel, muscle-type nicotinic receptor, TRANSPORT PROTEIN-INHIBITOR complex, General anesthetic, Inhibitor ;; TRANSPORT PROTEIN/INHIBITOR
Experimental Method method	ELECTRON MICROSCOPY

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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.

8f6y__assembly_1__model_1

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

Download this curve (.dat)

8f6y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8f6y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.68 Å
Rg (electron density)	43.97 Å
Total Rg	44.16 Å
Atom count	17048
Residues	2022
Excluded volume	309900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8f6y__assembly_1__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 (14)

Entity 1 Entity 1 polymer

Description description	Acetylcholine receptor subunit alpha
Molecular weight formula_weight	49766.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	17053

SEHETRLVANLLENYNKVIRPVEHHTHFVDITVGLQLIQLISVDEVNQIVETNVRLRQQWIDVRLRWNPADYGGIKKIRLPSDDVWLPDLVLYNNADGDFAIVHMTKLLLDYTGKIMWTPPAIFKSYCEIIVTHFPFDQQNCTMKLGIWTYDGTKVSISPESDRPDLSTFMESGEWVMKDYRGWKHWVYYTCCPDTPYLDITYHFIMQRIPLYFVVNVIIPCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMIFVISSIIITVVVINTHHRSPSTHTMPQWVRKIFIDTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQVTGEVIFQTPLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSVFAGRLIEL

Entity 2 Entity 2 polymer

Description description	Acetylcholine receptor subunit delta
Molecular weight formula_weight	57554.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VNEEERLINDLLIVNKYNKHVRPVKHNNEVVNIALSLTLSNLISLKETDETLTSNVWMDHAWYDHRLTWNASEYSDISILRLPPELVWIPDIVLQNNNDGQYHVAYFCNVLVRPNGYVTWLPPAIFRSSCPINVLYFPFDWQNCSLKFTALNYDANEITMDLMTDTIDGKDYPIEWIIIDPEAFTENGEWEIIHKPAKKNIYPDKFPNGTNYQDVTFYLIIRRKPLFYVINFITPCVLISFLASLAFYLPAESGEKMSTAISVLLAQAVFLLLTSQRLPETALAVPLIGKYLMFIMSLVTGVIVNCGIVLNFHFRTPSTHVLSTRVKQIFLEKLPRILHMSRADESEQPDWQNDLKLRRSSSVGYISKAQEYFNIKSRSELMFEKQSERHGLVPRVTPRIGFGNNNENIAASDQLHDEIKSGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFIFVMGNFNHPPAKPFEGDPFDYSSDHPRC

Entity 3 Entity 3 polymer

Description description	Acetylcholine receptor subunit beta
Molecular weight formula_weight	53731.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAWTDYRLQWDPAAYEGIKDLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQPSAIYRSSCTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAFTENGQWSIEHKPSRKNWRSDDPSYEDVTFYLIIQRKPLFYIVYTIIPCILISILAILVFYLPPDAGEKMSLSISALLAVTVFLLLLADKVPETSLSVPIIIRYLMFIMILVAFSVILSVVVLNLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRPVTTPSPDSKPTIISRANDEYFIRKPAGDFVCPVDNARVAVQPERLFSEMKWHLNGLTQPVTLPQDLKEAVEAIKYIAEQLESASEFDDLKKDWQYVAMVADRLFLYVFFVICSIGTFSIFLDASHNVPPDNPFA

Entity 4 Entity 4 polymer

Description description	Acetylcholine receptor subunit gamma
Molecular weight formula_weight	56335.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

ENEEGRLIEKLLGDYDKRIIPAKTLDHIIDVTLKLTLTNLISLNEKEEALTTNVWIEIQWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLVYNDGSMYWLPPAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNLQLSAEEGEAVEWIHIDPEDFTENGEWTIRHRPAKKNYNWQLTKDDTDFQEIIFFLIIQRKPLFYIINIIAPCVLISSLVVLVYFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGKYLIFVMFVSMLIVMNCVIVLNVSLRTPNTHSLSEKIKHLFLGFLPKYLGMQLEPSEETPEKPQPRRRSSFGIMIKAEEYILKKPRSELMFEEQKDRHGLKRVNKMTSDIDIGTTVDLYKDLANFAPEIKSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSIGTLAIFLTGHFNQVPEFPFPGDPRKYVP

Entity 5 Entity 5 branched

Description description	;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 ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	Etomidate
Molecular weight formula_weight	244.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	CHOLINE ION
Molecular weight formula_weight	104.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 13 Entity 13 non-polymer

Description description	nonane
Molecular weight formula_weight	128.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	8f6yA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	8f6yA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	8f6yB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	8f6yC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	8f6yD01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

Domain ID domain_id	8f6yD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	390 — Neurotransmitter-gated ion-channel transmembrane domain

Domain ID domain_id	8f6yE01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Neurotransmitter-gated ion-channel ligand-binding domain

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.79 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1413199

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate, desensitized-like state

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

Acetylcholine receptor subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acetylcholine receptor subunit delta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acetylcholine receptor subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acetylcholine receptor subunit gamma

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

8f6y__assembly_1__model_1

8f6y__assembly_1__model_1 | I(q)

8f6y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)