SAXSdb — 9zco

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

Transient receptor potential cation channel subfamily M member 8

Parus major

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 6–1098 Chain B； UniProt 6–1098 Chain C； UniProt 6–1098 Chain D； UniProt 6–1098	Not recorded	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.45 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 9ZCO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9P7S Avian TRPM8 (Parus major) closed, ligand-free structure resolved in cell vesicles using cryo-EM Deposited 2025-06-21	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9P90 Avian TRPM8 (Parus major) desensitized, fully-swapped, ligand-free structure resolved in cell vesicles using cryo-EM Deposited 2025-06-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9P91 Avian TRPM8 (Parus major) semi-swapped, ligand-free structure resolved in cell vesicles using cryo-EM Deposited 2025-06-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9PAR Avian TRPM8 (Parus major) semi-swapped, ligand-free structure at high pH and 4 degrees Celsius resolved in GDN using cryo-EM Deposited 2025-06-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9PB6 Avian TRPM8 (Parus major) menthol bound structure resolved in cell vesicles using cryo-EM Deposited 2025-06-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	XUQ (1R,2S,5R)-5-methyl-2-(propan-2-yl)cyclohexan-1-ol × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9ZCN Avian TRPM8 (Parus major) fully-swapped, closed, ligand-free in the presence of calcium, structure resolved in cell vesicles Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9ZCP Avian TRPM8 (Parus major) fully swapped closed, calcium free, in the presence of menthol, resolved in cell vesicles Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
9ZCQ Avian TRPM8 (Parus major) semi-swapped, closed, calcium free, menthol bound structure resolved in cell vesicles Deposited 2025-11-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	XUQ (1R,2S,5R)-5-methyl-2-(propan-2-yl)cyclohexan-1-ol × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
9ZCR Parus major TRPM8 with a chimeric human outer pore loops, semi-swapped, ligand-free, cold, structure resolved in GDN Deposited 2025-11-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 4–1098（1095 aa） Chain B 4–1098（1095 aa） Chain C 4–1098（1095 aa） Chain D 4–1098（1095 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9ZEZ Avian TRPM8 (Parus major) semi-swapped, calcium free, menthol bound structure resolved in cell vesicles Deposited 2025-12-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 6–1098（1093 aa） Chain B 6–1098（1093 aa） Chain C 6–1098（1093 aa） Chain D 6–1098（1093 aa）	Not recorded	XUQ (1R,2S,5R)-5-methyl-2-(propan-2-yl)cyclohexan-1-ol × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A5S8WF66_PARMJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–1101； UniProt 6–1098 Author chain B； PDBConstruct 9–1101； UniProt 6–1098 Author chain C； PDBConstruct 9–1101； UniProt 6–1098 Author chain D； PDBConstruct 9–1101； UniProt 6–1098

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	9zco
Deposition date deposition_date	2025-11-24
Structure title title	Avian TRPM8 (Parus major) semi-swapped, closed, ligand-free in the presence of calcium, structure resolved in cell vesicles
Keywords keywords	TRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, Parus major; 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	53.61 Å
Radius of gyration Rg (electron density) rg_electron	52.97 Å
Forward intensity I(0) i0	2502580000.00
Molecular weight molecular_weight	439470.0 kDa
Excluded volume excluded_volume	557340 Å³
Envelope volume envelope_volume	851680 Å³
Hydration-shell volume shell_volume	129410 Å³
Envelope diameter envelope_diameter	163.9 Å
Shell Rg shell_rg	61.21 Å
Envelope Rg envelope_rg	50.52 Å
Shape Rg shape_rg	52.97 Å
Total Rg total_rg	53.24 Å
Total atoms total_atoms	61240
Residues n_residues	3896
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	167.5 Å
Rg (real space) rg_real	53.28 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	2.5030e+09
I(0) uncertainty (real space) i0_real_error	4.7760e+07
Rg (reciprocal space) rg_reciprocal	53.88 Å
I(0) (reciprocal space) i0_reciprocal	2505000000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.3 Å
Skewness Skewness skewness	0.021
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	289800000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.904

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Transient receptor potential cation channel subfamily M member 8
Molecular weight formula_weight	127217.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	61240

GPGSGSGMRHRRNGNFESSRLLYSSMSRSIDVACSDADLANFIQENFKKRECVFFTKDTKSMGNLCKCGYPENQHIEGTQVNTTEKWNYKKHTKELPTDAFGDIQFENLGKRGKYIRLSCDTDSETLYDLMTQHWHLKTPNLVISVTGGAKNFALKPRMRKIFSRLIYIAQSKGAWIFTGGTHYGLMKYIGEVVRDNTISRSSEENVVAIGIAAWGMISNRETLIRTADSDGSFLARYIMDDLKRDPLYCLDNNHTHLLLVDNGTHGHPTTEAKVRTQLEKYISERVIPESNYGGKIPIVCFAQGGGKETLKSINVAIKSKIPCVVVEGSGRIADVIASLVEAEGTLASSCVKESLLRFLPRTISRLSEEETESWIKWIKEVLESPHLLTVIKIEEAGDEIVSNAISFALYKAFSTNEHDRDNWNGQLKLLLEWNQLDLASDEIFTNDRNWESADLQDVMFTALVKDRPKFVRLFLENGLNLRKFLTTEVLRELYTNNFSSLVFKNLQIAKNSYNDALLTFVWKMVEDFRRGFKRDYKNSKDEMEIQLSEECPITRHPLQALFIWSVLQNKKELSKVIWEQTRGCTLAALGASKLLKSMAKVKNDINAAGESEELANEYETRAVELFTECYSNDEDLAEQLLTYSCEAWGGSNCLELAVEARDQQFIAQPGVQNFLSKQWYGEISRDTKNWKIIMCLFFFPLIGCGFISFRKKPVEKSKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFVLLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDRCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRLTIPFPFVIFAYIFMVMRKCFKCCCNKESKEPSICCSRNEDNEILAWEAVMKENYLVKINTKANDSSEEMVHRFRQLDAKLSDLKGLLKEISSKIK

来源 Source

来源生物 organism	Parus major
通用名 common_name	Great Tit
NCBI Class编号 ncbi_taxonomy_id	9157
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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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	3.45 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	61895

fit	/app/data/saxs_computation/zc/9zco/9zco.fit
pddf	/app/data/pr_computation/zc/9zco/9zco.pr.out
profile	/app/data/saxs_computation/zc/9zco/9zco.dat

Avian TRPM8 (Parus major) semi-swapped, closed, ligand-free in the presence of calcium, structure resolved in cell vesicles

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

Transient receptor potential cation channel subfamily M member 8

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)