SAXSdb — 6yio

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

Interleukin-2 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 B； UniProt 22–213	Not recorded	FAB FRAGMENT HEAVY CHAIN × 1 FAB FRGAMENT LIGHT CHAIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；25% v/v PEG Smear Medium (12.5% w/v PEG 3350, 12.5% w/v PEG 4000, 12.5% w/v PEG 2000, 12.5% w/v PEG 5000 MME) 0.1M SODIUM ACETATE, PH 4.5	Resolution 1.83 Å R-free 0.231

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 6YIO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z92 structure of interleukin-2 with its alpha receptor Deposited 2005-03-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–238（217 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Na-malonic acid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.280
2B5I cytokine receptor complex Deposited 2005-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 22–238（217 aa）	Mutation：N68Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.269
2ERJ Crystal structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 Deposited 2005-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–233（212 aa）	Mutation：N49S,N68S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；295.5 K；MPEG 550, sodium acetate, sodium citrate, phenol, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K	Resolution 3.00 Å R-free 0.263
2ERJ Crystal structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 Deposited 2005-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 22–233（212 aa）	Mutation：N49S,N68S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；295.5 K；MPEG 550, sodium acetate, sodium citrate, phenol, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K	Resolution 3.00 Å R-free 0.263
3IU3 Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain Deposited 2009-08-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 22–238（217 aa） Fragment：Extracellular domain, ectodomain, UNP residues 22-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.262
3IU3 Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain Deposited 2009-08-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 22–238（217 aa） Fragment：Extracellular domain, ectodomain, UNP residues 22-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.262
3IU3 Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain Deposited 2009-08-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 22–238（217 aa） Fragment：Extracellular domain, ectodomain, UNP residues 22-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.262
3NFP Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain Deposited 2010-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 22–238（217 aa） Fragment：UNP residues 22-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.86 Å R-free 0.301
3NFP Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain Deposited 2010-06-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 22–238（217 aa） Fragment：UNP residues 22-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.86 Å R-free 0.301
6VWU X-ray structure of ALKS 4230, a fusion of circularly permuted human Interleukin-2 and Interleukin-2 Receptor alpha Deposited 2020-02-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–186（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；An equal volume of protein was mixed with crystallization buffer, 25 % (w/v) PEG 3350, 0.2 M MgCl2, 0.1 M Hepes 7.5. Large crystals appeared within 48-72 hours, and were frozen in a cryoprotectant consisting of mother liquor with 10 % glycerol	Resolution 3.40 Å R-free 0.297
7F9W CD25 in complex with Fab Deposited 2021-07-05	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–186（161 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZMZ Engineered Interleukin 2 bound to CD25 receptor Deposited 2022-04-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 21–238（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；19% PEG 3350, 0.2 M Sodium tartrate dibasic dihydrate, 10% glycerol	Resolution 3.20 Å R-free 0.258
9KMC Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 and anti-CD25 Fab S417 Deposited 2024-11-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 22–240（219 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL2RA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–192； UniProt 22–213

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	6yio
Deposition date deposition_date	2020-04-01
Structure title title	CRYSTAL STRUCTURE OF FAB RG6292 IN COMPLEX WITH CD25 ECD
Keywords keywords	ANTIBODY, CD25 ECD, FAB RG6292, IL2Ra, 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	31.22 Å
Radius of gyration Rg (electron density) rg_electron	30.87 Å
Forward intensity I(0) i0	62703900.00
Molecular weight molecular_weight	61115.0 kDa
Excluded volume excluded_volume	75934 Å³
Envelope volume envelope_volume	103290 Å³
Hydration-shell volume shell_volume	29897 Å³
Envelope diameter envelope_diameter	114.2 Å
Shell Rg shell_rg	35.57 Å
Envelope Rg envelope_rg	31.15 Å
Shape Rg shape_rg	30.82 Å
Total Rg total_rg	31.45 Å
Total atoms total_atoms	4289
Residues n_residues	563
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	106.1 Å
Rg (real space) rg_real	31.52 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	6.2700e+07
I(0) uncertainty (real space) i0_real_error	9.7190e+05
Rg (reciprocal space) rg_reciprocal	31.39 Å
I(0) (reciprocal space) i0_reciprocal	62700000.0000
Solution quality estimate total_estimate	0.8486
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.548
Kurtosis Kurtosis kurtosis	-0.243
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6061000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.754; Smooth: 0.834

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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-2 receptor subunit alpha
Molecular weight formula_weight	23219.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4924

ELCDDDPPEIPHATFKAMAYKEGTMLNCECKRGFRRIKSGSLYMLCTGNSSHSSWDNQCQCTSSATRNTTKQVTPQPEEQKERKTTEMQSPMQPVDQASLPGHCREPPPWENEATERIYHFVVGQMVYYQCVQGYRALHRGPAESVCKMTHGKTRWTQPQLICTGEMETSQFPGEEKPQASPEGRPESETSCAHHHHHHHHHH

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	FAB FRAGMENT HEAVY CHAIN
Molecular weight formula_weight	23646.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSLAISWVRQAPGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARGGSVSGTLVDFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

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	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	FAB FRGAMENT LIGHT CHAIN
Molecular weight formula_weight	23397.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNIYPITFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	Cricetulus griseus

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	589

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6yiob1
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d6yiob2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.1 — Complement control module/SCR domain

Domain ID domain_id	d6yioh_
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	d6yiol1
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	d6yiol2
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 (4 domains)

Domain ID domain_id	6yioH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6yioH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6yioL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6yioL02
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	51.381 Å
Unit-cell length b length_b	44.321 Å
Unit-cell length c length_c	140.085 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	69.980 Å
R factor r_factor	0.2039
R_work r_work	0.2025
R_free r_free	0.2309

fit	/app/data/saxs_computation/yi/6yio/6yio.fit
pddf	/app/data/pr_computation/yi/6yio/6yio.pr.out
profile	/app/data/saxs_computation/yi/6yio/6yio.dat

CRYSTAL STRUCTURE OF FAB RG6292 IN COMPLEX WITH CD25 ECD

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

Interleukin-2 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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)