SAXSdb — 3di2

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

Interleukin-7

Homo sapiens

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 × 2 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） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 26–177	Fragment：UNP residues 26 to 177 Mutation：E106A	Interleukin-7 receptor subunit alpha × 1 （P16871）	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

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 3DI2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DI3 Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 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 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

1 other PDB entries and 1 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 Author chain C； 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	Protein heterocomplex Heteromer Protein × 2 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） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 21–239	Fragment：UNP residues 21 to 239 (ligand binding ectodomain) Mutation：I118V	Interleukin-7 × 1 （P13232）	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

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 3DI2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DI3 Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 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
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 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 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 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 11 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 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3di2
Deposition date deposition_date	2008-06-19
Structure title title	Crystal structure of the complex of human interleukin-7 with unglycosylated human interleukin-7 receptor alpha ectodomain
Keywords keywords	;interleukin, cytokine, cytokine receptor, ectodomain, Glycoprotein, Growth factor, Secreted, Alternative splicing, Disease mutation, Membrane, Phosphoprotein, Polymorphism, Receptor, SCID, Transmembrane, CYTOKINE-CYTOKINE RECEPTOR COMPLEX ;; CYTOKINE/CYTOKINE RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	43.78 Å
Radius of gyration Rg (electron density) rg_electron	43.65 Å
Forward intensity I(0) i0	65606400.00
Molecular weight molecular_weight	67931.0 kDa
Excluded volume excluded_volume	85709 Å³
Envelope volume envelope_volume	135180 Å³
Hydration-shell volume shell_volume	26770 Å³
Envelope diameter envelope_diameter	140.4 Å
Shell Rg shell_rg	47.44 Å
Envelope Rg envelope_rg	41.30 Å
Shape Rg shape_rg	43.61 Å
Total Rg total_rg	43.99 Å
Total atoms total_atoms	4790
Residues n_residues	616
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	133.7 Å
Rg (real space) rg_real	44.03 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	6.5610e+07
I(0) uncertainty (real space) i0_real_error	1.1850e+06
Rg (reciprocal space) rg_reciprocal	43.78 Å
I(0) (reciprocal space) i0_reciprocal	65590000.0000
Solution quality estimate total_estimate	0.7654
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.896
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2168000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.624; Smooth: 0.133

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Interleukin-7
Molecular weight formula_weight	17545.5 kDa
Mutation mutation	E106A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4818

MGDCDIEGKDGKQYESVLMVSIDQLLDSMKEIGSNCLNNEFNFFKRHICDANKEGMFLFRAARKLRQFLKMNSTGDFDLHLLKVSEGTTILLNCTGQVKGRKPAALGAAQPTKSLEENKSLKEQKKLNDLCFLKRLLQEIKTCWNKILMGTKEH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Interleukin-7 receptor subunit alpha
Molecular weight formula_weight	25691.0 kDa
Mutation mutation	I118V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GSHMESGYAQNGDLEDAELDDYSFSCYSQLEVNGSQHSLTCAFEDPDVNTTNLEFEICGALVEVKCLNFRKLQEIYFIETKKFLLIGKSNICVKVGEKSLTCKKIDLTTIVKPEAPFDLSVVYREGANDFVVTFNTSHLQKKYVKVLMHDVAYRQEKDENKWTHVNLSSTKLTLLQRKLQPAAMYEIKVRSIPDHYFKGFWSEWSPSYYFRTPEINNSSGEMD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3di2A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3di2B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1870 —

Domain ID domain_id	3di2B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3di2C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3di2D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1870 —

Domain ID domain_id	3di2D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	47.202 Å
Unit-cell length b length_b	113.021 Å
Unit-cell length c length_c	87.534 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2670

fit	/app/data/saxs_computation/di/3di2/3di2.fit
pddf	/app/data/pr_computation/di/3di2/3di2.pr.out
profile	/app/data/saxs_computation/di/3di2/3di2.dat

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

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

Interleukin-7

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-7 receptor subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)