← Back to search
3bpo

Crystal structure of the IL13-IL4R-IL13Ra ternary complex

Method: X-RAY DIFFRACTION Dmax: 99.2 Å Quality: GOOD
▼

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

Interleukin 13

Homo sapiens

UniProt Q4VB50

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 × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 20–145 Not recorded Interleukin-4 receptor alpha chain × 1 （P24394） Interleukin-13 receptor alpha-1 chain × 1 （P78552） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；12% PEG8K, 8% ethlyene glycol, 0.1M ammonium citrate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 3.00 Å R-free 0.312

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.

Other PDB Difference from Current Entry 3BPO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8BLQ Cryo-EM structure of the CODV-IL13-RefAb triple complex Deposited 2022-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 24–132（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q4VB50_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–127； UniProt 20–145

Interleukin-4 receptor alpha chain

Homo sapiens

UniProt P24394

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 × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 27–227 Fragment：Extracellular domain, residues 27-227 Interleukin 13 × 1 （Q4VB50） Interleukin-13 receptor alpha-1 chain × 1 （P78552） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；12% PEG8K, 8% ethlyene glycol, 0.1M ammonium citrate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 3.00 Å R-free 0.312

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.

Other PDB Difference from Current Entry 3BPO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IAR INTERLEUKIN-4 / RECEPTOR ALPHA CHAIN COMPLEX Deposited 1999-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–232（207 aa） Fragment：EXTRACELLULAR DOMAIN
Mutation：M1F, C182A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.30 Å R-free 0.289
1IRS IRS-1 PTB DOMAIN COMPLEXED WITH A IL-4 RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 489–499（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
3BPL Crystal structure of the IL4-IL4R-Common Gamma ternary complex Deposited 2007-12-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 27–227（201 aa） Fragment：Extracellular domain, residues 27-227
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；10% PEG8K, 8% ethylene glycol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.93 Å R-free 0.297
3BPN Crystal structure of the IL4-IL4R-IL13Ra ternary complex Deposited 2007-12-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 27–227（201 aa） Fragment：Extracellular domain, residues 27-227
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；10% PEG8K, 0.1M cacodylate pH 6.5, 0.16M calcium acetate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.02 Å R-free 0.304
5E4E Engineered Interleukin-13 bound to receptor Deposited 2015-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 26–228（203 aa） Fragment：UNP residues 26-228
Not recorded SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；lithium sulfate, phosphate/citrate pH 4.2, PEG 1000
Resolution 3.00 Å R-free 0.288
6OEL Engineered Fab bound to IL-4 receptor Deposited 2019-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 27–224（198 aa） Fragment：UNP residues 27-224
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；22.5% PurePEG (Microlytic), 0.1 M sodium citrate, pH 5.5, 0.6 M ammonium nitrate
Resolution 3.10 Å R-free 0.256
6WGL Dupilumab fab with Crystal Kappa design complexed with human IL-4 receptor Deposited 2020-04-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 26–232（207 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；100mM Hepes pH 7.5, 25% PEG MME 550
Resolution 2.82 Å R-free 0.304
8Z8L structure of IL-4Ra in complex with an nanobody 4E9 Deposited 2024-04-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–232（207 aa）
Mutation：C182A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；1.4 M Sodium malonate dibasic monohydrate pH 6.0
Resolution 3.96 Å R-free 0.334

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

View Construct and Data Evidence
UniProt name IL4RA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–205； UniProt 27–227

Interleukin-13 receptor alpha-1 chain

Homo sapiens

UniProt P78552

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 × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 29–342 Fragment：Extracellular domain, residues 29-342 Interleukin 13 × 1 （Q4VB50） Interleukin-4 receptor alpha chain × 1 （P24394） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；12% PEG8K, 8% ethlyene glycol, 0.1M ammonium citrate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 3.00 Å R-free 0.312

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.

Other PDB Difference from Current Entry 3BPO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BPN Crystal structure of the IL4-IL4R-IL13Ra ternary complex Deposited 2007-12-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 29–342（314 aa） Fragment：Extracellular domain, residues 29-342
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；10% PEG8K, 0.1M cacodylate pH 6.5, 0.16M calcium acetate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.02 Å R-free 0.304
4HWB Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment Deposited 2012-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 223–336（114 aa）
Not recorded SO4 SULFATE ION × 13 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；1.6-2.0 M Li2SO4 0.1M CHES pH9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.61 Å R-free 0.224
5E4E Engineered Interleukin-13 bound to receptor Deposited 2015-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 23–340（318 aa） Fragment：UNP residues 23-340
Not recorded SO4 SULFATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.2；293 K；lithium sulfate, phosphate/citrate pH 4.2, PEG 1000
Resolution 3.00 Å R-free 0.288

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I13R1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–314； UniProt 29–342

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 3bpo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bpo
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3bpo
Deposition date deposition_date2007-12-18
Structure title titleCrystal structure of the IL13-IL4R-IL13Ra ternary complex
Keywords keywords;IL4, IL13, IL4R, IL13R, cytokine, receptor, Glycoprotein, Immune response, Membrane, Phosphoprotein, Secreted, Transmembrane, Cytokine-Cytokine receptor COMPLEX ;; Cytokine/Cytokine receptor
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier30.60 Å
Radius of gyration Rg (electron density) rg_electron29.77 Å
Forward intensity I(0) i067700100.00
Molecular weight molecular_weight64218.0 kDa
Excluded volume excluded_volume80073 ų
Envelope volume envelope_volume108200 ų
Hydration-shell volume shell_volume31271 ų
Envelope diameter envelope_diameter103.1 Å
Shell Rg shell_rg35.70 Å
Envelope Rg envelope_rg29.83 Å
Shape Rg shape_rg29.76 Å
Total Rg total_rg30.37 Å
Total atoms total_atoms4520
Residues n_residues582
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax99.2 Å
Rg (real space) rg_real30.61 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real6.7700e+07
I(0) uncertainty (real space) i0_real_error1.1030e+06
Rg (reciprocal space) rg_reciprocal30.61 Å
I(0) (reciprocal space) i0_reciprocal67700000.0000
Solution quality estimate total_estimate0.8991
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3 Å
Skewness Skewness skewness0.302
Kurtosis Kurtosis kurtosis-0.462
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8001000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.900
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3bpoa_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.2 — Short-chain cytokines
Domain ID domain_idd3bpob1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd3bpob2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd3bpob3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id3bpoA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3bpoB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bpoB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bpoC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bpoC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bpoC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)