SAXSdb — 6p50

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

Interleukin-7 receptor subunit alpha

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 21–239	Not recorded	anti-IL-7R 4A10 Fab heavy chain × 1 anti-IL-7R 4A10 Fab light chain × 1 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

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 6P50	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 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 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 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 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
3DI3 Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain Deposited 2008-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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
6P67 Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha 2B8 Fab Deposited 2019-06-03	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 oligomeric state 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 oligomeric state 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 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 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 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 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 ligand/ion 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	1
Chains and sequence ranges	Author chain C； 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	6p50
Deposition date deposition_date	2019-05-29
Structure title title	Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10
Keywords keywords	Interleukin-7 receptor extracellular dohmain, Antibody 4A10 Fab fragment, protein polymer, IMMUNE SYSTEM; IMMUNE SYSTEM
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	29.10 Å
Radius of gyration Rg (electron density) rg_electron	28.83 Å
Forward intensity I(0) i0	52435100.00
Molecular weight molecular_weight	56720.0 kDa
Excluded volume excluded_volume	70881 Å³
Envelope volume envelope_volume	92652 Å³
Hydration-shell volume shell_volume	28511 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	34.14 Å
Envelope Rg envelope_rg	29.09 Å
Shape Rg shape_rg	28.82 Å
Total Rg total_rg	29.37 Å
Total atoms total_atoms	3990
Residues n_residues	522
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	100.9 Å
Rg (real space) rg_real	29.34 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	5.2440e+07
I(0) uncertainty (real space) i0_real_error	8.5080e+05
Rg (reciprocal space) rg_reciprocal	29.24 Å
I(0) (reciprocal space) i0_reciprocal	52430000.0000
Solution quality estimate total_estimate	0.8411
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.598
Kurtosis Kurtosis kurtosis	-0.039
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8865000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.770

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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 receptor subunit alpha
Molecular weight formula_weight	25691.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	3990

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	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	anti-IL-7R 4A10 Fab heavy chain
Molecular weight formula_weight	24360.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQPGAELVMPGASVKLSCKASGYTFTSYWMHWVKQRPGEGLEWIGEIDPSDSYTNDNQKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARRLYSNSYYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDCG

Entity 3 Entity 3 polymer

Description description	anti-IL-7R 4A10 Fab light chain
Molecular weight formula_weight	23606.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSSLSASLGGKVTITCKASQDIKKYIAWYQHKPGKGPRLLIHYTSTLQPGIPSRFSGSGSGRDYSFSISNLEPVDIATYYCLQYDNLLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPRDINVKWKIDGSERQNGVLNSWTDQDSKDSTYNMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6p50h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6p50h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6p50l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6p50l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	6p50C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1870 —

Domain ID domain_id	6p50H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6p50L02
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	145.113 Å
Unit-cell length b length_b	40.171 Å
Unit-cell length c length_c	105.097 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	38.610 Å
R factor r_factor	0.2879
R_work r_work	0.2855
R_free r_free	0.3298

fit	/app/data/saxs_computation/p5/6p50/6p50.fit
pddf	/app/data/pr_computation/p5/6p50/6p50.pr.out
profile	/app/data/saxs_computation/p5/6p50/6p50.dat

Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10

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

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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)