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9pb6

Avian TRPM8 (Parus major) menthol bound structure resolved in cell vesicles using cryo-EM

Method: ELECTRON MICROSCOPY Dmax: 158.7 Å Quality: GOOD
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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

UniProt A0A5S8WF66

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 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

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 9PB6 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
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
9ZCO Avian TRPM8 (Parus major) semi-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 CA CALCIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 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 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 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9pb6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9pb6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9pb6
Deposition date deposition_date2025-06-26
Structure title titleAvian TRPM8 (Parus major) menthol bound structure resolved in cell vesicles using cryo-EM
Keywords keywordsTRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, menthol; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.75 Å
Radius of gyration Rg (electron density) rg_electron51.35 Å
Forward intensity I(0) i02310390000.00
Molecular weight molecular_weight424010.0 kDa
Excluded volume excluded_volume538620 ų
Envelope volume envelope_volume790460 ų
Hydration-shell volume shell_volume123670 ų
Envelope diameter envelope_diameter163.8 Å
Shell Rg shell_rg59.58 Å
Envelope Rg envelope_rg49.20 Å
Shape Rg shape_rg51.36 Å
Total Rg total_rg51.60 Å
Total atoms total_atoms59188
Residues n_residues3748
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax158.7 Å
Rg (real space) rg_real51.45 Å
Rg uncertainty (real space) rg_real_error0.76 Å
I(0) (real space) i0_real2.3100e+09
I(0) uncertainty (real space) i0_real_error3.8120e+07
Rg (reciprocal space) rg_reciprocal52.00 Å
I(0) (reciprocal space) i0_reciprocal2312000000.0000
Solution quality estimate total_estimate0.8812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.8 Å
Skewness Skewness skewness0.025
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha283000000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.798
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)