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3va2

Crystal structure of human Interleukin-5 in complex with its alpha receptor

Method: X-RAY DIFFRACTION Dmax: 90.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interleukin-5

Homo sapiens

UniProt P05113

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 A； UniProt 23–134 Chain B； UniProt 23–134 Fragment：UNP residues 23-134 Interleukin-5 receptor subunit alpha × 1 （Q01344） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.276

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 3VA2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HUL A NOVEL DIMER CONFIGURATION REVEALED BY THE CRYSTAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF HUMAN INTERLEUKIN-5 Deposited 1995-03-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–131（108 aa）
Chain B 24–131（108 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.369
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 19–134（116 aa）
Chain D 19–134（116 aa）
Not recorded BGC beta-D-glucopyranose × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.55 Å R-free 0.264
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 19–134（116 aa）
Chain F 19–134（116 aa）
Not recorded BGC beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.55 Å R-free 0.264
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26 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 C 20–134（115 aa）
Chain D 20–134（115 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9GVN DEPEMOKIMAB FAB IN COMPLEX WITH INTERLEUKIN 5 Deposited 2024-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 20–134（115 aa）
Chain B 20–134（115 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Morpheus EDO_P8K, Morpheus Carboxylic acids, Morpheus buffer system 2
Resolution 1.93 Å R-free 0.209

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

View Construct and Data Evidence
UniProt name IL5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–119； UniProt 23–134 Author chain B； PDBConstruct 8–119； UniProt 23–134

Interleukin-5 receptor subunit alpha

Homo sapiens

UniProt Q01344

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 21–335 Fragment：ectodomain, UNP residues 21-335 Interleukin-5 × 2 （P05113） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.70 Å R-free 0.276

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 3VA2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1OBX Crystal structure of the complex of PDZ2 of syntenin with an interleukin 5 receptor alpha peptide. Deposited 2003-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 413–420（8 aa） Fragment：LAST 8 RESIDUES, RESIDUES 413-420
Not recorded CO COBALT (II) ION × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP 0.1 M HEPES, PH 7.0, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, 0.2 M MGSO4 WITH MICROSEEDIN
Resolution 1.35 Å R-free 0.212
1OBZ Crystal structure of the complex of the PDZ tandem of syntenin with an interleukin 5 receptor alpha peptide. Deposited 2003-01-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 413–420（8 aa） Fragment：LAST 8 RESIDUES, RESIDUES 413-420
Not recorded ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；SITTING DROP WITH 0.2 M SODIUM ACETATE, PH 4.6 28% PEG4000, 0.2 M AMMONIUM ACETATE
Resolution 1.70 Å R-free 0.213
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–335（316 aa）
Mutation：C66A, K72M, L138M, K167M, L234M BGC beta-D-glucopyranose × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.55 Å R-free 0.264
3QT2 Structure of a cytokine ligand-receptor complex Deposited 2011-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–335（316 aa）
Mutation：C66A, K72M, L138M, K167M, L234M BGC beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.55 Å R-free 0.264
6H41 Structure of the complex of the IL-5 inhibitory peptide AF17121 bound to the IL-5 receptor IL-5Ralpha Deposited 2018-07-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–335（309 aa）
Mutation：C66A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；0.1 M sodium acetate pH 5.0, 3% (w/v) PEG 4000, 15% - 20% (v/v) 2-methyl-2,4-pentanediol
Resolution 2.75 Å R-free 0.226
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26 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 F 21–341（321 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL5RA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 8–322； UniProt 21–335

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 3va2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3va2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3va2
Deposition date deposition_date2011-12-28
Structure title titleCrystal structure of human Interleukin-5 in complex with its alpha receptor
Keywords keywords;cytokine, eosinophilic, asthma, JAK/STAT, fibronectin III-like (Fn III) domain, canonical cytokine receptor homology module (CRM), B cell growth, Ig secretion, eosinophils proliferation, cell surface, CYTOKINE-CYTOKINE RECEPTOR complex ;; CYTOKINE/CYTOKINE RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.11 Å
Radius of gyration Rg (electron density) rg_electron27.20 Å
Forward intensity I(0) i057118900.00
Molecular weight molecular_weight59618.0 kDa
Excluded volume excluded_volume75028 ų
Envelope volume envelope_volume95307 ų
Hydration-shell volume shell_volume30239 ų
Envelope diameter envelope_diameter99.5 Å
Shell Rg shell_rg33.29 Å
Envelope Rg envelope_rg27.35 Å
Shape Rg shape_rg27.20 Å
Total Rg total_rg27.85 Å
Total atoms total_atoms4203
Residues n_residues523
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.0 Å
Rg (real space) rg_real28.03 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real5.7120e+07
I(0) uncertainty (real space) i0_real_error8.6950e+05
Rg (reciprocal space) rg_reciprocal28.05 Å
I(0) (reciprocal space) i0_reciprocal57120000.0000
Solution quality estimate total_estimate0.7891
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary37.0 Å
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.361
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11560000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.760; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3va2a_
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_idd3va2b_
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

CATH v4.4 (5 domains)

Domain ID domain_id3va2A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3va2B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3va2C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3va2C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3va2C03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)