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3di3

Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain

Method: X-RAY DIFFRACTION Dmax: 80.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Interleukin-7

Homo sapiens

UniProt P13232

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 × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–177 Fragment：UNP residues 26 to 177 Mutation：E106A Interleukin-7 receptor subunit alpha × 1 （P16871） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；292 K；18% w/v PEG 3350, 0.1 M HEPES pH 7.4, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.90 Å R-free 0.267

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 3DI3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DI2 Crystal structure of the complex of human interleukin-7 with unglycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–177（152 aa） Fragment：UNP residues 26 to 177
Mutation：E106A 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；20% w/v PEG 8000, 0.1M MES, 0.2 M calcium acetate, pH 6.0, sitting drop, temperature 292K
Resolution 2.70 Å R-free 0.267
3DI2 Crystal structure of the complex of human interleukin-7 with unglycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 26–177（152 aa） Fragment：UNP residues 26 to 177
Mutation：E106A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；20% w/v PEG 8000, 0.1M MES, 0.2 M calcium acetate, pH 6.0, sitting drop, temperature 292K
Resolution 2.70 Å R-free 0.267

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IL7_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–154； UniProt 26–177

Interleukin-7 receptor subunit alpha

Homo sapiens

UniProt P16871

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 × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 21–239 Fragment：UNP residues 21 to 239 (ligand binding ectodomain) Mutation：I118V Interleukin-7 × 1 （P13232） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.4；292 K；18% w/v PEG 3350, 0.1 M HEPES pH 7.4, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.90 Å R-free 0.267

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 3DI3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DI2 Crystal structure of the complex of human interleukin-7 with unglycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19 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 21–239（219 aa） Fragment：UNP residues 21 to 239 (ligand binding ectodomain)
Mutation：I118V 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；20% w/v PEG 8000, 0.1M MES, 0.2 M calcium acetate, pH 6.0, sitting drop, temperature 292K
Resolution 2.70 Å R-free 0.267
3DI2 Crystal structure of the complex of human interleukin-7 with unglycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 21–239（219 aa） Fragment：UNP residues 21 to 239 (ligand binding ectodomain)
Mutation：I118V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；292 K；20% w/v PEG 8000, 0.1M MES, 0.2 M calcium acetate, pH 6.0, sitting drop, temperature 292K
Resolution 2.70 Å R-free 0.267
3UP1 Crystal structure of the unliganded human interleukin-7 receptor extracellular domain Deposited 2011-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–239（219 aa）
Chain B 21–239（219 aa）
Not recorded FUC alpha-L-fucopyranose × 2 SO4 SULFATE ION × 5 GOL GLYCEROL × 4 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；292 K；1.26M (NH4)2SO4, 0.1 M Tris-HCl pH 8.5, 0.2 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.15 Å R-free 0.257
6P50 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10 Deposited 2019-05-29 Different construct Different mutation/modification 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 21–239（219 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；25% PEG 3350, 0.2 M sodium malonate pH 6.0, 20% glycerol
Resolution 2.90 Å R-free 0.330
6P67 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab Deposited 2019-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 21–239（219 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；17% PEG 3350, 10% MPD, 0.2 lithium sulfate, 0.1 M imidazole pH 6.5, 20% glycerol
Resolution 2.90 Å R-free 0.266
6P67 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab Deposited 2019-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 21–239（219 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；17% PEG 3350, 10% MPD, 0.2 lithium sulfate, 0.1 M imidazole pH 6.5, 20% glycerol
Resolution 2.90 Å R-free 0.266
6P67 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab Deposited 2019-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 21–239（219 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；17% PEG 3350, 10% MPD, 0.2 lithium sulfate, 0.1 M imidazole pH 6.5, 20% glycerol
Resolution 2.90 Å R-free 0.266
6P67 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab Deposited 2019-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 21–239（219 aa）
Not recorded FUC alpha-L-fucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；17% PEG 3350, 10% MPD, 0.2 lithium sulfate, 0.1 M imidazole pH 6.5, 20% glycerol
Resolution 2.90 Å R-free 0.266
7OPB IL7R in complex with an antagonist Deposited 2021-05-31 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 A 36–231（196 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0,1 M Phosphate/Citrate, 25% v/v PEG Smear Low Cryoprotected with 25% PEG-400
Resolution 2.14 Å R-free 0.211
7OPB IL7R in complex with an antagonist Deposited 2021-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–231（196 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0,1 M Phosphate/Citrate, 25% v/v PEG Smear Low Cryoprotected with 25% PEG-400
Resolution 2.14 Å R-free 0.211
7OPB IL7R in complex with an antagonist Deposited 2021-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 36–231（196 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0,1 M Phosphate/Citrate, 25% v/v PEG Smear Low Cryoprotected with 25% PEG-400
Resolution 2.14 Å R-free 0.211
9XEA Structure of the transmembrane domain dimer of human IL-7R V253G mutant Deposited 2025-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 236–266（31 aa）
Chain B 236–266（31 aa）
Mutation：V253G Mutation：V253G No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；306 K；Ionic strength (raw mmCIF value) 25；Pressure 1
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N; U-85% 2H] The transmembrane domain of the IL-7R-V253G dimer, 60 mM POPC, 150 mM DHPC, 25 mM MES, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mM [U-13C; U-15N] Transmembrane domain of the IL-7R V253G mutant, 60 mM deuterated Deuterated POPC, 150 mM deuterated Deuterated DHPC, 25 mM MES, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM [U-15N; U-2H] Transmembrane domain of the IL-7R V253G mutant, 0.4 mM [U-13C] Transmembrane domain of the IL-7R V253G mutant, 60 mM deuterated Deuterated POPC, 150 mM deuterated Deuterated DHPC, 25 mM MES, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name IL7RA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–223； UniProt 21–239

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 3di3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3di3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3di3
Deposition date deposition_date2008-06-19
Structure title titleCrystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain
Keywords keywords;interleukin, cytokine, cytokine receptor, ectodomain, Glycoprotein, Growth factor, Secreted, Disease mutation, Membrane, Phosphoprotein, Receptor, SCID, Transmembrane, 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_guinier25.28 Å
Radius of gyration Rg (electron density) rg_electron24.42 Å
Forward intensity I(0) i020545000.00
Molecular weight molecular_weight35273.0 kDa
Excluded volume excluded_volume44484 ų
Envelope volume envelope_volume56343 ų
Hydration-shell volume shell_volume20676 ų
Envelope diameter envelope_diameter83.7 Å
Shell Rg shell_rg29.78 Å
Envelope Rg envelope_rg24.84 Å
Shape Rg shape_rg24.42 Å
Total Rg total_rg25.13 Å
Total atoms total_atoms2485
Residues n_residues311
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 dmax80.8 Å
Rg (real space) rg_real25.35 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real2.0540e+07
I(0) uncertainty (real space) i0_real_error3.0790e+05
Rg (reciprocal space) rg_reciprocal25.33 Å
I(0) (reciprocal space) i0_reciprocal20540000.0000
Solution quality estimate total_estimate0.8909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.4 Å
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.3150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4898000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.897
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3di3A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily50 —
Domain ID domain_id3di3B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1870 —
Domain ID domain_id3di3B02
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)