8ddw

cryo-EM structure of TRPM3 ion channel in complex with Gbg, tethered by ALFA-nanobody

Method: ELECTRON MICROSCOPY Dmax: 183.1 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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 1–1371 Chain B; UniProt 1–1371 Chain C; UniProt 1–1371 Chain D; UniProt 1–1371 Not recorded Unidentified segment at the N-terminus of TRPM3 × 4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.70 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 1–1371; UniProt 1–1371 Author chain B; PDBConstruct 1–1371; UniProt 1–1371 Author chain C; PDBConstruct 1–1371; UniProt 1–1371 Author chain D; PDBConstruct 1–1371; UniProt 1–1371

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

Homo sapiens

UniProt P62873

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain I; UniProt 2–340 Not recorded Transient receptor potential cation channel, subfamily M, member 3 × 4 (Q5F4S7) Unidentified segment at the N-terminus of TRPM3 × 4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 × 1 (P59768) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.70 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.

1260 other PDB entries and 1263 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBB1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain I; PDBConstruct 1–339; UniProt 2–340

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Homo sapiens

UniProt P59768

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain J; UniProt 2–71 Mutation:C68S Transient receptor potential cation channel, subfamily M, member 3 × 4 (Q5F4S7) Unidentified segment at the N-terminus of TRPM3 × 4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 × 1 (P62873) ELECTRON MICROSCOPY cryo-EM buffer:pH 8.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.70 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.

1233 other PDB entries and 1236 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBG2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain J; PDBConstruct 1–70; UniProt 2–71

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 8ddw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8ddw
Deposition date deposition_date2022-06-19
Structure title titlecryo-EM structure of TRPM3 ion channel in complex with Gbg, tethered by ALFA-nanobody
Keywords keywordsTRPM3, ion channel, Gbg, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier53.79
Radius of gyration Rg (electron density) rg_electron53.50
Forward intensity I(0) i01937040000.00
Molecular weight molecular_weight368160.0 kDa
Excluded volume excluded_volume461360 ų
Envelope volume envelope_volume735540 ų
Hydration-shell volume shell_volume114340 ų
Envelope diameter envelope_diameter185.9
Shell Rg shell_rg58.35
Envelope Rg envelope_rg51.37
Shape Rg shape_rg53.51
Total Rg total_rg53.64
Total atoms total_atoms25863
Residues n_residues3266
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 dmax183.1
Rg (real space) rg_real53.70
Rg uncertainty (real space) rg_real_error1.43
I(0) (real space) i0_real1.9370e+09
I(0) uncertainty (real space) i0_real_error4.1570e+07
Rg (reciprocal space) rg_reciprocal53.85
I(0) (reciprocal space) i0_reciprocal1937000000.0000
Solution quality estimate total_estimate0.8462
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.5
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.132
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha201500000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.786

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)