SAXSdb — 2na9

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

Cytokine receptor common subunit beta

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 432–473	Fragment：Helical transmembrane residues 432-473	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；313 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N; 80% 2H] protein, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

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 2NA9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8P NMR STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE COMMON BETA-CHAIN IN THE GM-CSF, IL-3 AND IL-5 RECEPTORS Deposited 1999-10-05	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 338–438（101 aa） Fragment：DOMAIN 4	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；293 K；Ionic strength (raw mmCIF value) 0.06M；Pressure AMBIENT NMR sample composition 0.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;90% H2O, 10% D2O NMR sample composition 0.4MM D4BC U-15N; 10MM PHOSPHATE BUFFER;100% D2O	Resolution not provided
1EGJ DOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN ANTIBODY Deposited 2000-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 338–438（101 aa） Fragment：DOMAIN 4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；12% peg 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 2.80 Å R-free 0.288
1GH7 CRYSTAL STRUCTURE OF THE COMPLETE EXTRACELLULAR DOMAIN OF THE BETA-COMMON RECEPTOR OF IL-3, IL-5, AND GM-CSF Deposited 2000-11-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–437（413 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 25–437（413 aa） Fragment：EXTRACELLULAR DOMAIN	Mutation：N328Q Mutation：N328Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG MME 5000, Phosphate, pH 6.5, VAPOR DIFFUSION/HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.307
2NA8 Transmembrane Structure of the Cytokine Receptor Common Subunit beta Deposited 2015-12-21	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 432–473（42 aa） Fragment：Helical transmembrane residues 432-473	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；313 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N; 80% 2H] protein, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
4NKQ Structure of a Cytokine Receptor Complex Deposited 2013-11-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 25–438（414 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；100mM HEPES buffer (pH 7.0), 6%(v/v) PEG3350, 0.2M proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.273
5DWU Beta common receptor in complex with a Fab Deposited 2015-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 17–240（224 aa） Chain B 241–443（203 aa）	Mutation：N106Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M Tris 8, 25% - 35% PEG200	Resolution 3.97 Å R-free 0.330
6NMY A Cytokine-receptor complex Deposited 2019-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 25–240（216 aa） Chain B 241–438（198 aa）	Mutation：N346Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277.15 K；Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride	Resolution 3.30 Å R-free 0.278
6NMY A Cytokine-receptor complex Deposited 2019-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 25–240（216 aa） Chain D 241–438（198 aa）	Mutation：N346Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277.15 K；Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride	Resolution 3.30 Å R-free 0.278
8TLD Structure of the IL-5 Signaling Complex Deposited 2023-07-26	Different construct Different mutation/modification 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 B 23–442（420 aa） Chain E 23–442（420 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

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

View Construct and Data Evidence

UniProt name	IL3RB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–44； UniProt 432–473

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	2na9
Deposition date deposition_date	2015-12-21
Structure title title	Transmembrane Structure of the P441A Mutant of the Cytokine Receptor Common Subunit beta
Keywords keywords	transmembrane helix, NBP residue, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	20.33 Å
Radius of gyration Rg (electron density) rg_electron	19.48 Å
Forward intensity I(0) i0	123952000.00
Molecular weight molecular_weight	107480.0 kDa
Excluded volume excluded_volume	140650 Å³
Envelope volume envelope_volume	27709 Å³
Hydration-shell volume shell_volume	10738 Å³
Envelope diameter envelope_diameter	79.7 Å
Shell Rg shell_rg	28.55 Å
Envelope Rg envelope_rg	24.89 Å
Shape Rg shape_rg	19.47 Å
Total Rg total_rg	19.84 Å
Total atoms total_atoms	15855
Residues n_residues	924
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	74.0 Å
Rg (real space) rg_real	20.87 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.2400e+08
I(0) uncertainty (real space) i0_real_error	1.8070e+06
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	123900000.0000
Solution quality estimate total_estimate	0.5400
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	5
Primary peak position r_peak_primary	6.3 Å
Skewness Skewness skewness	0.454
Kurtosis Kurtosis kurtosis	-0.883
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12360.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.003; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.009; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Cytokine receptor common subunit beta
Molecular weight formula_weight	5120.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15855

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

fit	/app/data/saxs_computation/na/2na9/2na9.fit
pddf	/app/data/pr_computation/na/2na9/2na9.pr.out
profile	/app/data/saxs_computation/na/2na9/2na9.dat

Transmembrane Structure of the P441A Mutant of the Cytokine Receptor Common Subunit beta

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

Cytokine receptor common subunit beta

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)