8ddr

cryo-EM structure of TRPM3 ion channel in the absence of PIP2

Method: ELECTRON MICROSCOPY Dmax: 167.7 Å Quality: GOOD

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

Transient receptor potential cation channel, subfamily M, member 3

Mus musculus

UniProt Q5F4S7

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 2–1344 Chain B; UniProt 2–1344 Chain C; UniProt 2–1344 Chain D; UniProt 2–1344 Not recorded Unidentified segment at the N-terminus of TRPM3 × 4 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 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.

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5F4S7_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1343; UniProt 2–1344 Author chain B; PDBConstruct 1–1343; UniProt 2–1344 Author chain C; PDBConstruct 1–1343; UniProt 2–1344 Author chain D; PDBConstruct 1–1343; UniProt 2–1344

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 8ddr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ddr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ddr
Deposition date deposition_date2022-06-18
Structure title titlecryo-EM structure of TRPM3 ion channel in the absence of PIP2
Keywords keywordsTRPM3, ion channel, PIP2, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier53.66
Radius of gyration Rg (electron density) rg_electron53.39
Forward intensity I(0) i02644680000.00
Molecular weight molecular_weight455620.0 kDa
Excluded volume excluded_volume580100 ų
Envelope volume envelope_volume903010 ų
Hydration-shell volume shell_volume134410 ų
Envelope diameter envelope_diameter166.8
Shell Rg shell_rg62.92
Envelope Rg envelope_rg51.17
Shape Rg shape_rg53.41
Total Rg total_rg53.60
Total atoms total_atoms32042
Residues n_residues3940
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax167.7
Rg (real space) rg_real53.31
Rg uncertainty (real space) rg_real_error1.03
I(0) (real space) i0_real2.6450e+09
I(0) uncertainty (real space) i0_real_error5.0920e+07
Rg (reciprocal space) rg_reciprocal53.94
I(0) (reciprocal space) i0_reciprocal2647000000.0000
Solution quality estimate total_estimate0.8776
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary75.2
Skewness Skewness skewness0.019
Kurtosis Kurtosis kurtosis-0.492
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha395900000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.880

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)