← Back to search
9bpv

Structure of the IFN-lambda3/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta

Method: ELECTRON MICROSCOPY Dmax: 91.4 Å Quality: EXCELLENT
▼

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

Interleukin-10 receptor subunit beta

Homo sapiens

UniProt Q08334

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 A； UniProt 20–220 Not recorded Interferon lambda receptor 1 × 1 （Q8IU57） Interferon lambda-3 × 1 （Q8IZI9） 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

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 9BPV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LQM Structure of the IL-10R2 Common Chain Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–220（201 aa） 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
3LQM Structure of the IL-10R2 Common Chain Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 20–220（201 aa） 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
5T5W Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex Deposited 2016-08-31 Different construct Different mutation/modification 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） 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 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 oligomeric state Different ligand/ion 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

4 other PDB entries and 5 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 3–203； UniProt 20–220

Interferon lambda receptor 1

Homo sapiens

UniProt Q8IU57

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 21–226 Not recorded Interleukin-10 receptor subunit beta × 1 （Q08334） Interferon lambda-3 × 1 （Q8IZI9） 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

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 9BPV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5IXD Structure of human JAK1 FERM/SH2 in complex with IFN lambda receptor Deposited 2016-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 250–299（50 aa） Fragment：UNP residues 250-299
Not recorded CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1-0.2 M Ammonium Citrate tribasic pH 7, 5-15% PEG 3350
Resolution 2.85 Å R-free 0.282
5IXI Structure of human JAK1 FERM/SH2 in complex with IFNLR1/IL10RA chimera Deposited 2016-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 250–259（10 aa） Fragment：UNP residues 250-259,UNP residues 263-303
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M MES pH6.5, 0.2M MgCl2, 9% PEG4K, 25% ethylene glycol
Resolution 2.57 Å R-free 0.255
5L04 STRUCTURE OF INTERFERON LAMBDA 1 RECEPTOR WITH HUMAN KINASE JAK1 Deposited 2016-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 260–307（48 aa） Fragment：unp residues 260-307
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；7 mg/ml of protein in 50 mM Hepes buffer (pH 7.5) with 150 mM NaCl, mixesd with 1:1 ratio with 18% (w/v) PEG 3350, 0.2 M amonium formate
Resolution 2.10 Å R-free 0.230
5T5W Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex Deposited 2016-08-31 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–226（206 aa） Fragment：UNP residues 21-230
Not recorded 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
9BPU Structure of the IFN-lambda4/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta Deposited 2024-05-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–226（206 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INLR1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–206； UniProt 21–226

Interferon lambda-3

Homo sapiens

UniProt Q8IZI9

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 34–196 Not recorded Interleukin-10 receptor subunit beta × 1 （Q08334） Interferon lambda receptor 1 × 1 （Q8IU57） 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

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 9BPV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3HHC Interferon-lambda is functionally an interferon but structurally related to the IL-10 family Deposited 2009-05-15 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 5–200（196 aa）
Chain C 5–200（196 aa）
Not recorded IOD IODIDE ION × 23 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；285 K；28 % w/v PEG 4000, 200 mM ammonium sulfate, 3 % v/v isopropyl alcohol , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Resolution 2.80 Å R-free 0.314
3HHC Interferon-lambda is functionally an interferon but structurally related to the IL-10 family Deposited 2009-05-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 5–200（196 aa）
Chain D 5–200（196 aa）
Not recorded IOD IODIDE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；285 K；28 % w/v PEG 4000, 200 mM ammonium sulfate, 3 % v/v isopropyl alcohol , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Resolution 2.80 Å R-free 0.314
5T5W Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex Deposited 2016-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 34–195（162 aa） Fragment：UNP residues 34-195
Mutation：Q15R, E73D, H120R, T150A, V163E 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

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IFNL3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–165； UniProt 34–196

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9bpv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bpv
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9bpv
Deposition date deposition_date2024-05-08
Structure title titleStructure of the IFN-lambda3/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta
Keywords keywordsINTERFERON, CYTOKINE, CYTOKINE RECEPTOR, TYPE III INTERFERON; CYTOKINE
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.02 Å
Radius of gyration Rg (electron density) rg_electron28.17 Å
Forward intensity I(0) i063340900.00
Molecular weight molecular_weight62770.0 kDa
Excluded volume excluded_volume78725 ų
Envelope volume envelope_volume98258 ų
Hydration-shell volume shell_volume30068 ų
Envelope diameter envelope_diameter97.6 Å
Shell Rg shell_rg34.25 Å
Envelope Rg envelope_rg28.42 Å
Shape Rg shape_rg28.16 Å
Total Rg total_rg28.81 Å
Total atoms total_atoms4417
Residues n_residues542
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax91.4 Å
Rg (real space) rg_real29.00 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real6.3340e+07
I(0) uncertainty (real space) i0_real_error7.5800e+05
Rg (reciprocal space) rg_reciprocal29.01 Å
I(0) (reciprocal space) i0_reciprocal63340000.0000
Solution quality estimate total_estimate0.9074
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2 Å
Skewness Skewness skewness0.253
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8604000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.926
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▶

8. Citations (1)

▶

9. Files and Curves (10)