8u3a

TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)

Method: ELECTRON MICROSCOPY Dmax: 82.3 Å Quality: GOOD

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

Transient receptor potential cation channel subfamily V member 1

Rattus norvegicus

UniProt O35433

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 110–764 Chain D; UniProt 110–764 Not recorded VPN (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.30 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.

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPV1_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–635; UniProt 110–764 Author chain D; PDBConstruct 4–635; UniProt 110–764

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 8u3a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8u3a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8u3a
Deposition date deposition_date2023-09-07
Structure title titleTRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
Keywords keywordsTRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer), MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier24.92
Radius of gyration Rg (electron density) rg_electron23.87
Forward intensity I(0) i032227300.00
Molecular weight molecular_weight48730.0 kDa
Excluded volume excluded_volume63057 ų
Envelope volume envelope_volume75087 ų
Hydration-shell volume shell_volume26316 ų
Envelope diameter envelope_diameter82.7
Shell Rg shell_rg31.02
Envelope Rg envelope_rg24.34
Shape Rg shape_rg23.87
Total Rg total_rg24.77
Total atoms total_atoms6934
Residues n_residues405
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 dmax82.3
Rg (real space) rg_real24.85
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real3.2230e+07
I(0) uncertainty (real space) i0_real_error4.2640e+05
Rg (reciprocal space) rg_reciprocal24.87
I(0) (reciprocal space) i0_reciprocal32230000.0000
Solution quality estimate total_estimate0.8969
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.4
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6569000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)