8jmt

Structure of the adhesion GPCR ADGRL3 in the apo state

Method: ELECTRON MICROSCOPY Dmax: 64.7 Å Quality: GOOD

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

Adhesion G protein-coupled receptor L3,Soluble cytochrome b562

Homo sapiens

UniProt E7ES20

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 500–1051 Chain A; UniProt 1061–1132 Mutation:T364A/M566W/H654I No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen NITROGEN Resolution 3.36 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name E7ES20_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 9–560; UniProt 500–1051 Author chain A; PDBConstruct 662–733; UniProt 1061–1132

Adhesion G protein-coupled receptor L3,Soluble cytochrome b562

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 24–65 Chain A; UniProt 77–128 Mutation:T364A/M566W/H654I No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen NITROGEN Resolution 3.36 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 561–602; UniProt 24–65 Author chain A; PDBConstruct 607–660; UniProt 77–128

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 8jmt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8jmt
Deposition date deposition_date2023-06-05
Structure title titleStructure of the adhesion GPCR ADGRL3 in the apo state
Keywords keywordsADGRL3, Apo form, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier19.75
Radius of gyration Rg (electron density) rg_electron18.64
Forward intensity I(0) i09979360.00
Molecular weight molecular_weight26851.0 kDa
Excluded volume excluded_volume35093 ų
Envelope volume envelope_volume40134 ų
Hydration-shell volume shell_volume18214 ų
Envelope diameter envelope_diameter66.0
Shell Rg shell_rg24.85
Envelope Rg envelope_rg19.15
Shape Rg shape_rg18.62
Total Rg total_rg19.79
Total atoms total_atoms1894
Residues n_residues234
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 dmax64.7
Rg (real space) rg_real19.72
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real9.9790e+06
I(0) uncertainty (real space) i0_real_error1.3630e+05
Rg (reciprocal space) rg_reciprocal19.72
I(0) (reciprocal space) i0_reciprocal9979000.0000
Solution quality estimate total_estimate0.8132
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.7
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.360
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1630000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)