3bpl

Crystal structure of the IL4-IL4R-Common Gamma ternary complex

Method: X-RAY DIFFRACTION Dmax: 99.0 Å Quality: GOOD

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

Interleukin-4

Homo sapiens

UniProt P05112

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 2 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–153 Not recorded Interleukin-4 receptor alpha chain × 1 (P24394) Cytokine receptor common gamma chain × 1 (P31785) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 × 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

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.

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

View Construct and Data Evidence
UniProt name IL4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 25–153

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 2 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 27–227 Fragment:Extracellular domain, residues 27-227 Interleukin-4 × 1 (P05112) Cytokine receptor common gamma chain × 1 (P31785) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 × 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

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 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

Cytokine receptor common gamma chain

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 Other combination Heteromer Protein × 3 其他Polymer 2 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 56–254 Fragment:Extracellular domain, residues 56-254 Interleukin-4 × 1 (P05112) Interleukin-4 receptor alpha chain × 1 (P24394) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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 × 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

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 29 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 1–199; UniProt 56–254

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 3bpl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bpl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bpl
Deposition date deposition_date2007-12-18
Structure title titleCrystal structure of the IL4-IL4R-Common Gamma ternary complex
Keywords keywords;IL4, IL13, receptor, cytokine, B-cell activation, Glycoprotein, Growth factor, Secreted, Immune response, Membrane, Phosphoprotein, Transmembrane, Disease mutation, Host-virus interaction, SCID, Cytokine-receptor COMPLEX, 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_guinier29.12
Radius of gyration Rg (electron density) rg_electron28.34
Forward intensity I(0) i065608300.00
Molecular weight molecular_weight62426.0 kDa
Excluded volume excluded_volume77637 ų
Envelope volume envelope_volume100250 ų
Hydration-shell volume shell_volume30265 ų
Envelope diameter envelope_diameter105.7
Shell Rg shell_rg34.52
Envelope Rg envelope_rg28.54
Shape Rg shape_rg28.32
Total Rg total_rg29.01
Total atoms total_atoms4397
Residues n_residues522
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 dmax99.0
Rg (real space) rg_real29.13
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real6.5610e+07
I(0) uncertainty (real space) i0_real_error1.0450e+06
Rg (reciprocal space) rg_reciprocal29.13
I(0) (reciprocal space) i0_reciprocal65610000.0000
Solution quality estimate total_estimate0.8880
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.8
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.280
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10470000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.968

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3bpla_
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_idd3bplb1
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_idd3bplb2
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_idd3bplb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3bplc1
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_idd3bplc2
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

CATH v4.4 (5 domains)

Domain ID domain_id3bplA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10
Domain ID domain_id3bplB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bplB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bplC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3bplC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)