8x81

Structure of leptin-LepR trimer with a large gap

Method: ELECTRON MICROSCOPY Dmax: 195.8 Å Quality: GOOD

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

Leptin receptor

Homo sapiens

UniProt P48357

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 21–839 Chain B; UniProt 21–839 Chain C; UniProt 21–839 Not recorded Leptin × 3 (P41159) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.77 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.

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LEPR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–819; UniProt 21–839 Author chain B; PDBConstruct 1–819; UniProt 21–839 Author chain C; PDBConstruct 1–819; UniProt 21–839

Leptin

Homo sapiens

UniProt P41159

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 1 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 1–167 Chain E; UniProt 1–167 Chain F; UniProt 1–167 Not recorded Leptin receptor × 3 (P48357) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.77 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.

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LEP_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–167; UniProt 1–167 Author chain E; PDBConstruct 1–167; UniProt 1–167 Author chain F; PDBConstruct 1–167; UniProt 1–167

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 8x81

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8x81
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8x81
Deposition date deposition_date2023-11-27
Structure title titleStructure of leptin-LepR trimer with a large gap
Keywords keywordscytokine receptor, hexamer, CYTOKINE; CYTOKINE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier67.54
Radius of gyration Rg (electron density) rg_electron67.43
Forward intensity I(0) i01283810000.00
Molecular weight molecular_weight311180.0 kDa
Excluded volume excluded_volume393290 ų
Envelope volume envelope_volume819730 ų
Hydration-shell volume shell_volume104090 ų
Envelope diameter envelope_diameter217.8
Shell Rg shell_rg68.45
Envelope Rg envelope_rg62.89
Shape Rg shape_rg67.41
Total Rg total_rg67.56
Total atoms total_atoms21875
Residues n_residues2694
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 dmax195.8
Rg (real space) rg_real67.34
Rg uncertainty (real space) rg_real_error1.47
I(0) (real space) i0_real1.2840e+09
I(0) uncertainty (real space) i0_real_error2.6390e+07
Rg (reciprocal space) rg_reciprocal68.14
I(0) (reciprocal space) i0_reciprocal1286000000.0000
Solution quality estimate total_estimate0.8049
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary93.6
Skewness Skewness skewness0.080
Kurtosis Kurtosis kurtosis-0.210
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha67960000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.815; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.054

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)