SAXSdb — 3lqm

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

Interleukin-10 receptor 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 20–220	Fragment：Extracellular Domain Mutation：N49Q, N68Q, N102Q, C106S, S126C, N161Q	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.14 Å R-free 0.239
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 20–220	Fragment：Extracellular Domain Mutation：N49Q, N68Q, N102Q, C106S, S126C, N161Q	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.14 Å R-free 0.239

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 3LQM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5T5W Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex Deposited 2016-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–220（201 aa） Fragment：UNP residues 20-220	Mutation：N49Q, N68Q, N102Q, N161Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；.2 M Ca acetate, .1 M Imidazole pH 8.0, 10% PEG8000, 3% sucrose	Resolution 2.85 Å R-free 0.253
6X93 Interleukin-10 signaling complex with IL-10RA and IL-10RB Deposited 2020-06-02	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 × 6 PDB declaration: hexameric	Chain C 20–220（201 aa） Chain F 20–220（201 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；5s blotting	Resolution 3.50 Å
9BPU Structure of the IFN-lambda4/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta Deposited 2024-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–220（201 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9BPV Structure of the IFN-lambda3/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta Deposited 2024-05-08	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 × 3 PDB declaration: trimeric	Chain A 20–220（201 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	I10R2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–201； UniProt 20–220 Author chain B； PDBConstruct 1–201； UniProt 20–220

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	3lqm
Deposition date deposition_date	2010-02-09
Structure title title	Structure of the IL-10R2 Common Chain
Keywords keywords	;IL-10R2, receptor, common chain, cytokine, IL-10, IL-22, IL-26, IL-28, IL-29, Disulfide bond, Glycoprotein, Membrane, Phosphoprotein, Polymorphism, Transmembrane, Protein Binding ;; PROTEIN BINDING
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	35.07 Å
Radius of gyration Rg (electron density) rg_electron	35.90 Å
Forward intensity I(0) i0	39405500.00
Molecular weight molecular_weight	47626.0 kDa
Excluded volume excluded_volume	58609 Å³
Envelope volume envelope_volume	79042 Å³
Hydration-shell volume shell_volume	22907 Å³
Envelope diameter envelope_diameter	134.3 Å
Shell Rg shell_rg	33.23 Å
Envelope Rg envelope_rg	36.61 Å
Shape Rg shape_rg	35.86 Å
Total Rg total_rg	35.80 Å
Total atoms total_atoms	3339
Residues n_residues	397
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	128.6 Å
Rg (real space) rg_real	35.89 Å
Rg uncertainty (real space) rg_real_error	1.67 Å
I(0) (real space) i0_real	3.9410e+07
I(0) uncertainty (real space) i0_real_error	7.0560e+05
Rg (reciprocal space) rg_reciprocal	35.38 Å
I(0) (reciprocal space) i0_reciprocal	39390000.0000
Solution quality estimate total_estimate	0.6814
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.771
Kurtosis Kurtosis kurtosis	0.052
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2069000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.426; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.192; Smooth: 0.383

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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-10 receptor subunit beta
Molecular weight formula_weight	23583.4 kDa
Mutation mutation	N49Q, N68Q, N102Q, C106S, S126C, N161Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3551

MVPPPENVRMNSVNFKNILQWESPAFAKGQLTFTAQYLSYRIFQDKCMQTTLTECDFSSLSKYGDHTLRVRAEFADEHSDWVQITFSPVDDTIIGPPGMQVEVLADCLHMRFLAPKIENEYETWTMKNVYNSWTYNVQYWKQGTDEKFQITPQYDFEVLRNLEPWTTYCVQVRGFLPDRNKAGEWSEPVCEQTTHDETVPS

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	212

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3lqmA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3lqmA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3lqmB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3lqmB02
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	124.839 Å
Unit-cell length b length_b	124.839 Å
Unit-cell length c length_c	84.223 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2390

fit	/app/data/saxs_computation/lq/3lqm/3lqm.fit
pddf	/app/data/pr_computation/lq/3lqm/3lqm.pr.out
profile	/app/data/saxs_computation/lq/3lqm/3lqm.dat

Structure of the IL-10R2 Common Chain

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

Interleukin-10 receptor 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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction