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9zcr

Parus major TRPM8 with a chimeric human outer pore loops, semi-swapped, ligand-free, cold, structure resolved in GDN

Method: ELECTRON MICROSCOPY Dmax: 160.4 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 4–1098 Chain B； UniProt 4–1098 Chain C； UniProt 4–1098 Chain D； UniProt 4–1098 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.07 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 9ZCR 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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
9ZEZ Avian TRPM8 (Parus major) semi-swapped, calcium free, menthol bound structure resolved in cell vesicles Deposited 2025-12-01 Different construct 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 7–1101； UniProt 4–1098 Author chain B； PDBConstruct 7–1101； UniProt 4–1098 Author chain C； PDBConstruct 7–1101； UniProt 4–1098 Author chain D； PDBConstruct 7–1101； UniProt 4–1098

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 9zcr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9zcr
Deposition date deposition_date2025-11-24
Structure title titleParus major TRPM8 with a chimeric human outer pore loops, semi-swapped, ligand-free, cold, structure resolved in GDN
Keywords keywordsTRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, Human; 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_guinier51.18 Å
Radius of gyration Rg (electron density) rg_electron50.88 Å
Forward intensity I(0) i02174900000.00
Molecular weight molecular_weight410050.0 kDa
Excluded volume excluded_volume520540 ų
Envelope volume envelope_volume760820 ų
Hydration-shell volume shell_volume120410 ų
Envelope diameter envelope_diameter163.0 Å
Shell Rg shell_rg58.88 Å
Envelope Rg envelope_rg48.77 Å
Shape Rg shape_rg50.89 Å
Total Rg total_rg51.08 Å
Total atoms total_atoms57264
Residues n_residues3632
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 dmax160.4 Å
Rg (real space) rg_real50.89 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real2.1750e+09
I(0) uncertainty (real space) i0_real_error4.2840e+07
Rg (reciprocal space) rg_reciprocal51.40 Å
I(0) (reciprocal space) i0_reciprocal2176000000.0000
Solution quality estimate total_estimate0.8856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.3 Å
Skewness Skewness skewness0.035
Kurtosis Kurtosis kurtosis-0.493
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha275200000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)