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5t5w

Structure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex

Method: X-RAY DIFFRACTION Dmax: 92.3 Å Quality: EXCELLENT
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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 Fragment：UNP residues 20-220 Mutation：N49Q, N68Q, N102Q, N161Q Interferon lambda receptor 1 × 1 （Q8IU57） Interferon lambda-3 × 1 （Q8IZI9） 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

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 5T5W 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 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 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
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 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 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 Fragment：UNP residues 21-230 Interleukin-10 receptor subunit beta × 1 （Q08334） Interferon lambda-3 × 1 （Q8IZI9） 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

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 5T5W 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 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 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 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
9BPU Structure of the IFN-lambda4/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta Deposited 2024-05-08 Different construct 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 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
9BPV Structure of the IFN-lambda3/IFN-lambdaR1/IL-10Rbeta receptor complex with an engineered IL-10Rbeta Deposited 2024-05-08 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）
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

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 4–209； 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 34–195 Fragment：UNP residues 34-195 Mutation：Q15R, E73D, H120R, T150A, V163E Interleukin-10 receptor subunit beta × 1 （Q08334） Interferon lambda receptor 1 × 1 （Q8IU57） 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

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 5T5W 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 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 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
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 34–196（163 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

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 3–164； UniProt 34–195

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 5t5w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5t5w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5t5w
Deposition date deposition_date2016-08-31
Structure title titleStructure of an affinity matured lambda-IFN/IFN-lambdaR1/IL-10Rbeta receptor complex
Keywords keywordsreceptor, cytokine, CYTOKINE-CYTOKINE RECEPTOR complex; CYTOKINE/CYTOKINE RECEPTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.60 Å
Radius of gyration Rg (electron density) rg_electron27.79 Å
Forward intensity I(0) i058855100.00
Molecular weight molecular_weight60298.0 kDa
Excluded volume excluded_volume75521 ų
Envelope volume envelope_volume95030 ų
Hydration-shell volume shell_volume29511 ų
Envelope diameter envelope_diameter98.2 Å
Shell Rg shell_rg33.83 Å
Envelope Rg envelope_rg28.05 Å
Shape Rg shape_rg27.79 Å
Total Rg total_rg28.42 Å
Total atoms total_atoms4248
Residues n_residues537
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.3 Å
Rg (real space) rg_real28.57 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real5.8860e+07
I(0) uncertainty (real space) i0_real_error8.1350e+05
Rg (reciprocal space) rg_reciprocal28.59 Å
I(0) (reciprocal space) i0_reciprocal58860000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5 Å
Skewness Skewness skewness0.262
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8027000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5t5wA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t5wA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t5wB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5t5wB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)