9e2t

Structure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg

Method: X-RAY DIFFRACTION Dmax: 205.3 Å Quality: REASONABLE

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

Interleukin-21 receptor

Homo sapiens

UniProt Q9HBE5

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 20–228 Fragment:extracellular domain 21h10 × 1 Cytokine receptor common subunit gamma × 1 (P31785) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 20–228 Fragment:extracellular domain 21h10 × 1 Cytokine receptor common subunit gamma × 1 (P31785) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 20–228 Fragment:extracellular domain 21h10 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 20–228 Fragment:extracellular domain 21h10 × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242

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.

5 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL21R_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–212; UniProt 20–228 Author chain E; PDBConstruct 4–212; UniProt 20–228 Author chain H; PDBConstruct 4–212; UniProt 20–228 Author chain J; PDBConstruct 4–212; UniProt 20–228

Cytokine receptor common subunit gamma

Homo sapiens

UniProt P31785

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 55–254 Fragment:residues 55-254 21h10 × 1 Interleukin-21 receptor × 1 (Q9HBE5) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 55–254 Fragment:residues 55-254 21h10 × 1 Interleukin-21 receptor × 1 (Q9HBE5) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;298 K;0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350 Resolution 2.28 Å R-free 0.242

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.

13 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL2RG_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 4–203; UniProt 55–254 Author chain F; PDBConstruct 4–203; UniProt 55–254

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 9e2t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9e2t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9e2t
Deposition date deposition_date2024-10-22
Structure title titleStructure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg
Keywords keywordscytokine, immunology, interleukin, DE NOVO PROTEIN, DE NOVO PROTEIN-IMMUNE SYSTEM complex; DE NOVO PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier61.81
Radius of gyration Rg (electron density) rg_electron63.56
Forward intensity I(0) i0530020000.00
Molecular weight molecular_weight187850.0 kDa
Excluded volume excluded_volume233370 ų
Envelope volume envelope_volume357470 ų
Hydration-shell volume shell_volume54766 ų
Envelope diameter envelope_diameter226.1
Shell Rg shell_rg49.56
Envelope Rg envelope_rg63.82
Shape Rg shape_rg63.57
Total Rg total_rg63.09
Total atoms total_atoms13210
Residues n_residues1591
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 dmax205.3
Rg (real space) rg_real63.22
Rg uncertainty (real space) rg_real_error2.24
I(0) (real space) i0_real5.2990e+08
I(0) uncertainty (real space) i0_real_error1.1630e+07
Rg (reciprocal space) rg_reciprocal60.52
I(0) (reciprocal space) i0_reciprocal527600000.0000
Solution quality estimate total_estimate0.6955
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.1
Skewness Skewness skewness0.621
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha18740000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.503; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.511; Smooth: 0.023

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)