SAXSdb — 8yx8

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

Ligand-gated cation channel ZACN

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	Other combination Homooligomer Protein × 5 其他Polymer 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–412 Chain B； UniProt 1–412 Chain C； UniProt 1–412 Chain D； UniProt 1–412 Chain E； UniProt 1–412	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.80 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.

Other PDB	Difference from Current Entry 8YX8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YX6 Structure of a Cys-loop Receptor in Zinc Binding State Deposited 2024-04-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8YX7 Structure of a Cys-loop Receptor under Acidic Condition Deposited 2024-04-02	Parsed fields agree	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9LET Cryo-EM structure of human ZAC in zinc Binding State Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.62 Å
9LEU Cryo-EM structure of human ZAC with A152 mutant in zinc binding state Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
9LEV Cryo-EM structure of human ZAC in nanodisc in apo state Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9LEX Cryo-EM structure of human ZAC in zinc partially binding state in nanodisc Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
9LEY Cryo-EM structure of human ZAC in complex with d-tubocurarine Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	TC9 D-TUBOCURARINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9LEZ Cryo-EM structure of human ZAC in complex with N-(4-(tert-butyl)thiazol-2-yl)-3-fluorobenzamide (TTFB) Deposited 2025-01-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–412（412 aa） Chain B 1–412（412 aa） Chain C 1–412（412 aa） Chain D 1–412（412 aa） Chain E 1–412（412 aa）	Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T Mutation：A152T	A1EKJ ~{N}-(4-~{tert}-butyl-1,3-thiazol-2-yl)-3-fluoranyl-benzamide × 5 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ZACN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–412 Author chain B； PDBConstruct 1–420； UniProt 1–412 Author chain C； PDBConstruct 1–420； UniProt 1–412 Author chain D； PDBConstruct 1–420； UniProt 1–412 Author chain E； PDBConstruct 1–420； UniProt 1–412

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	8yx8
Deposition date deposition_date	2024-04-02
Structure title title	Structure of a Cys-loop Receptor in Apo State
Keywords keywords	Cys-loop Receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	37.35 Å
Radius of gyration Rg (electron density) rg_electron	36.59 Å
Forward intensity I(0) i0	459041000.00
Molecular weight molecular_weight	185250.0 kDa
Excluded volume excluded_volume	236460 Å³
Envelope volume envelope_volume	297450 Å³
Hydration-shell volume shell_volume	65693 Å³
Envelope diameter envelope_diameter	124.2 Å
Shell Rg shell_rg	44.48 Å
Envelope Rg envelope_rg	36.44 Å
Shape Rg shape_rg	36.59 Å
Total Rg total_rg	37.10 Å
Total atoms total_atoms	13070
Residues n_residues	1620
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	122.3 Å
Rg (real space) rg_real	37.25 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	4.5900e+08
I(0) uncertainty (real space) i0_real_error	7.5930e+06
Rg (reciprocal space) rg_reciprocal	37.31 Å
I(0) (reciprocal space) i0_reciprocal	459100000.0000
Solution quality estimate total_estimate	0.8709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.6 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94100000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.904

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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	Ligand-gated cation channel ZACN
Molecular weight formula_weight	46858.1 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	13070

MMALWSLLHLTFLGFSITLLLVHGQGFQGTAAIWPSDYKDDDDKLFNVNLSKKVQESIQIPNNGSAPLLVDVRVFVSNVFNVDILRYTMSSMLLLRLSWLDTRLAWNTSAHPRHAITLPWESLWTPRLTILEALWVDWRDQSPQARVDQDGHVKLNLALATETNCNFELLHFPRDHSNCSLSFYALSNTAMELEFQAHVVNEIVSVKREYVVYDLKTQVPPQQLVPCFQVTLRLKNTALKSIIALLVPAEALLLADVCGGLLPLRAIERIGYKVTLLLSYLVLHSSLVQALPSSSSCNPLLIYYFTILLLLLFLSTIETVLLAGLLARGNLGAKSGPSPAPRGEQREHGNPGPHPAEEPSRGVKGSQRSWPETADRIFFLVYVVGVLCTQFVFAGIWMWAACKSDAAPGEAAPHGRRPRL

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	Homo sapiens

Entity 2 Entity 2 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	5

Entity 3 Entity 3 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	5

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8. Citations (1)

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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	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	38022

fit	/app/data/saxs_computation/yx/8yx8/8yx8.fit
pddf	/app/data/pr_computation/yx/8yx8/8yx8.pr.out
profile	/app/data/saxs_computation/yx/8yx8/8yx8.dat

Structure of a Cys-loop Receptor in Apo State

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

Ligand-gated cation channel ZACN

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

冷冻电镜 EM 3D