SAXSdb — 5zk3

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

Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 10–217 Chain A； UniProt 377–466	Fragment：UNP residues 10-217,UNP residues 377-466 Mutation：S110R	QNB (3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；50mM MES-NaOH pH 6.2-7.0, 26-32% PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM QNB and 5% DMSO	Resolution 2.60 Å R-free 0.291

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.

Other PDB	Difference from Current Entry 5ZK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UON Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist Deposited 2011-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa） Fragment：UNP RESIDUES 1-217, UNP RESIDUES 2-161, UNP RESIDUES 377-466 Chain A 377–466（90 aa） Fragment：UNP RESIDUES 1-217, UNP RESIDUES 2-161, UNP RESIDUES 377-466	Mutation：N2D, N3D, N6D, N9D, C54T, C97A Mutation：N2D, N3D, N6D, N9D, C54T, C97A	QNB (3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate × 1 BGC beta-D-glucopyranose × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；25 to 35% PEG 300, 100 mM ammonium phosphate, 2% 2-Methyl-2,4-pentanediol, 100 mM HEPES, 10:1 monoolein:cholesterol lipid mix diluted 1.5:1 with protein in detergent buffer, Lipidic cubic phase, temperature 293K, pH 7.5	Resolution 3.00 Å R-free 0.276
4MQS Structure of active human M2 muscarinic acetylcholine receptor bound to the agonist iperoxo Deposited 2013-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa） Fragment：UNP residues 1-232, 373-466 Chain A 373–466（94 aa） Fragment：UNP residues 1-232, 373-466	Mutation：N0D, N1D, N4D, N7D, A373T, K374R Mutation：N0D, N1D, N4D, N7D, A373T, K374R	IXO 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 10 - 20% PEG300, 100 mM HEPES, pH 7.2 - 7.9, 1.2% 1,2,3-heptanetriol, and 20 - 80 mM EDTA, pH 8.0, Lipidic cubic phase, temperature 293K	Resolution 3.50 Å R-free 0.298
4MQT Structure of active human M2 muscarinic acetylcholine receptor bound to the agonist iperoxo and allosteric modulator LY2119620 Deposited 2013-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–232（232 aa） Fragment：UNP residues 1-232,373-466 Chain A 373–466（94 aa） Fragment：UNP residues 1-232,373-466	Mutation：N0D, N1D, N4D, N7D, A373T, K374R Mutation：N0D, N1D, N4D, N7D, A373T, K374R	IXO 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium × 1 2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 0.5 mM LY2119620, 10 - 20% PEG300, 100 mM HEPES pH 7.2 - 7.9, 1.2% 1,2,3-heptanetriol, and 20 - 80 mM EDTA pH 8.0, Lipidic cubic phase, temperature 293K	Resolution 3.70 Å R-free 0.301
5YC8 Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS (Hg-derivative) Deposited 2017-09-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–214（205 aa） Fragment：UNP residues 10-214,UNP residues 377-466 Chain A 377–466（90 aa） Fragment：UNP residues 10-214,UNP residues 377-466	Mutation：S110R Mutation：S110R	3C0 N-methyl scopolamine × 1 HG MERCURY (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50mM MES-NaOH pH 6.2-7.0, 26-32% PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM NMS and 5% DMSO, 1mM HgCl2	Resolution 2.50 Å R-free 0.270
5ZK8 Crystal structure of M2 muscarinic acetylcholine receptor bound with NMS Deposited 2018-03-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–217（208 aa） Fragment：UNP residues 10-217,UNP residues 377-466 Chain A 377–466（90 aa） Fragment：UNP residues 10-217,UNP residues 377-466	Not recorded	3C0 N-methyl scopolamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50mM MES-NaOH pH 6.2-7.0, 26-32 % PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM NMS and 5% DMSO	Resolution 3.00 Å R-free 0.270
5ZKB Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with AF-DX 384 Deposited 2018-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–217（208 aa） Fragment：UNP residues 10-217,UNP residues 377-466 Chain A 377–466（90 aa） Fragment：UNP residues 10-217,UNP residues 377-466	Mutation：S110R Mutation：S110R	82F N-[2-[(2S)-2-[(dipropylamino)methyl]piperidin-1-yl]ethyl]-6-oxidanylidene-5H-pyrido[2,3-b][1,4]benzodiazepine-11-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50mM MES-NaOH pH 6.2-7.0, 18 % PEG300, 100mM Magnesium acetate, 1% 1,2,3-heptanetriol, 0.5mM AF-DX 384 and 5% DMSO	Resolution 2.95 Å R-free 0.280
5ZKC Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with NMS Deposited 2018-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–217（208 aa） Fragment：UNP residues 10-217,UNP residues 377-466 Chain A 377–466（90 aa） Fragment：UNP residues 10-217,UNP residues 377-466	Mutation：S110R Mutation：S110R	3C0 N-methyl scopolamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50mM MES-NaOH pH 6.2-7.0, 26-32 % PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM NMS and 5% DMSO	Resolution 2.30 Å R-free 0.259
6OIK Muscarinic acetylcholine receptor 2-Go complex Deposited 2019-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 3–232（230 aa） Chain R 360–466（107 aa）	Mutation：N8A, N11D, N14D,N11D, N14D Mutation：N8A, N11D, N14D,N11D, N14D	IXO 4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium × 1 2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6U1N GPCR-Beta arrestin structure in lipid bilayer Deposited 2019-08-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 2–466（465 aa） Fragment：M2 UNP residues 2-466 + V2 UNP residues 343-371	Non-standard monomer：Yes (specific site not provided by mmCIF)	2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7T8X Cryo-EM structure of ACh-bound M2R-Go signaling complex in S1 state Deposited 2021-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 4–232（229 aa） Chain A 368–466（99 aa）	Not recorded	ACH ACETYLCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
7T90 Cryo-EM structure of ACh-bound M2R-Go signaling complex in S2 state Deposited 2021-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 4–232（229 aa） Chain A 368–466（99 aa）	Not recorded	ACH ACETYLCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
7T94 Cryo-EM structure of S1 state ACh-bound M2R-Go signaling complex with a PAM Deposited 2021-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 4–232（229 aa） Chain A 368–466（99 aa）	Not recorded	ACH ACETYLCHOLINE × 1 2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
7T96 Cryo-EM structure of S2 state ACh-bound M2R-Go signaling complex with a PAM Deposited 2021-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 4–232（229 aa） Chain A 368–466（99 aa）	Not recorded	ACH ACETYLCHOLINE × 1 2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8J8R Structure of beta-arrestin2 in complex with M2Rpp Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 300–317（18 aa） Fragment：ICL3 Chain U 300–317（18 aa） Fragment：ICL3 Chain V 300–317（18 aa） Fragment：ICL3	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8J97 Structure of Muscarinic receptor (M2R) in complex with beta-arrestin1 (Local refine, cross-linked) Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 305–313（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8JAF Structure of Muscarinic receptor (M2R) in complex with beta-arrestin1 (Local Refine, non-cross linked) Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain V 307–313（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACM2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–219； UniProt 10–217 Author chain A； PDBConstruct 326–415； UniProt 377–466

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	5zk3
Deposition date deposition_date	2018-03-23
Structure title title	Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with QNB
Keywords keywords	GPCR crystallography, rationally thermostabilized mutant, MEMBRANE PROTEIN-INHIBITOR complex; MEMBRANE PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.32 Å
Radius of gyration Rg (electron density) rg_electron	26.73 Å
Forward intensity I(0) i0	26555000.00
Molecular weight molecular_weight	43101.0 kDa
Excluded volume excluded_volume	55508 Å³
Envelope volume envelope_volume	70644 Å³
Hydration-shell volume shell_volume	23735 Å³
Envelope diameter envelope_diameter	93.1 Å
Shell Rg shell_rg	31.97 Å
Envelope Rg envelope_rg	26.86 Å
Shape Rg shape_rg	26.74 Å
Total Rg total_rg	27.37 Å
Total atoms total_atoms	3037
Residues n_residues	380
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	89.9 Å
Rg (real space) rg_real	27.56 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	2.6550e+07
I(0) uncertainty (real space) i0_real_error	3.7290e+05
Rg (reciprocal space) rg_reciprocal	27.49 Å
I(0) (reciprocal space) i0_reciprocal	26550000.0000
Solution quality estimate total_estimate	0.8718
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.4 Å
Skewness Skewness skewness	0.494
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3129000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.833

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2
Molecular weight formula_weight	47293.2 kDa
Mutation mutation	S110R
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	3048

GPMDDSTDSSDNSLALTSPYKTFEVVFIVLVAGSLSLVTIIGNILVMVSIKVNRHLQTVNNYFLFSLACADLIIGVFSMNLYTLYTVIGYWPLGPVVCDLWLALDYVVSNARVMNLLIISFDRYFCVTKPLTYPVKRTTKMAGMMIAAAWVLSFILWAPAILFWQFIVGVRTVEDGECYIQFFSNAAVTFGTAIAAFYLPVIIMTVLYWHISRASKSRIADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLPPPSREKKVTRTILAILLAFIITWAPYNVMVLINTFCAPCIPNTVWTIGYWLCYINSTINPACYALCNATFKKTFKHLLMCHYKNIGATRLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	(3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate
Molecular weight formula_weight	337.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 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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8. Citations (1)

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Unit-cell length a length_a	46.480 Å
Unit-cell length b length_b	58.800 Å
Unit-cell length c length_c	89.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	45.908 Å
R factor r_factor	0.2438
R_work r_work	0.2413
R_free r_free	0.2909

fit	/app/data/saxs_computation/zk/5zk3/5zk3.fit
pddf	/app/data/pr_computation/zk/5zk3/5zk3.pr.out
profile	/app/data/saxs_computation/zk/5zk3/5zk3.dat

Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with QNB

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

Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction