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5j12

Structure of human TSLP:TSLPR in complex with mouse IL-7Ralpha

Method: X-RAY DIFFRACTION Dmax: 90.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thymic stromal lymphopoietin

Homo sapiens

UniProt Q969D9

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 1–159 Mutation：N64Q,K126S + residues 127-131 were deleted Interleukin-7 receptor subunit alpha × 1 （P16872） Cytokine receptor-like factor 2 × 1 （Q9HC73） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.53 M ammonium sulfate 0.1 M sodium chloride 0.1 M BIS-TRIS pH 7.0 Resolution 3.55 Å R-free 0.225

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 5J12 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5J11 Structure of human TSLP in complex with TSLPR and IL-7Ralpha Deposited 2016-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–159（131 aa）
Mutation：Residues 127 to 131 were deleted in the construct used for crystallisation. PGE TRIETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；0.02 M Citric acid 0.08 M BIS-TRIS propane 16% w/v polyethylene glycol 3350
Resolution 2.56 Å R-free 0.218
5J13 Structural basis for TSLP antagonism by the therapeutic antibody Tezepelumab (MEDI9929 / AMG-157) Deposited 2016-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–159（131 aa）
Mutation：Residues 127 to 131 were deleted in the construct used for crystallisation. SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2 M ammonium sulfate 0.1 M sodium acetate pH 4.6 25% w/v polyethylene glycol 4000
Resolution 2.30 Å R-free 0.215
8QFZ TSLP-Bicycle complex Deposited 2023-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–155（127 aa）
Not recorded LFI 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG MME 500/PEG 20000, 0.1 M Carboxylic acids mix and 0.1 M Buffer system 3 pH 8.5
Resolution 1.65 Å R-free 0.210
8ZEU CryoEM structure of GR2002-F(ab')2: TSLP complex Deposited 2024-05-07 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 × 10 PDB declaration: decameric
Chain C 29–155（127 aa）
Chain G 29–155（127 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å

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

View Construct and Data Evidence
UniProt name TSLP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–154； UniProt 1–159

Interleukin-7 receptor subunit alpha

Mus musculus

UniProt P16872

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 21–239 Not recorded Thymic stromal lymphopoietin × 1 （Q969D9） Cytokine receptor-like factor 2 × 1 （Q9HC73） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.53 M ammonium sulfate 0.1 M sodium chloride 0.1 M BIS-TRIS pH 7.0 Resolution 3.55 Å R-free 0.225

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 5J12 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NN5 Cytokine receptor complex - Crystal form 1A Deposited 2013-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–239（219 aa） Fragment：extracellular domain (UNP residues 21-239)
Not recorded ACT ACETATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；293 K；14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.90 Å R-free 0.201
4NN6 Cytokine receptor complex - Crystal form 1B Deposited 2013-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–239（219 aa） Fragment：extracellular domain (UNP residues 21-239)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；293 K；14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, soaked in 18% PEG4000, 0.1 M Tris-HCl, pH 7.5, 0.3 M calcium acetate for 1 hour prior to cryoprotection, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.54 Å R-free 0.297
4NN7 Cytokine receptor complex - Crystal form 2 Deposited 2013-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–239（219 aa） Fragment：extracellular domain (UNP residues 21-239)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% pentaerythritol ethoxylate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.77 Å R-free 0.286
8DDC Intramembrane recognition between transmembrane domains of IL-7R and common gamma chain Deposited 2022-06-17 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 236–266（31 aa） Fragment：Transmembrane domain, residues 236-266
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 0.15；Pressure 1
NMR sample composition 0.4 mM 15N, 13C, 85%2H Transmembrane domain of the common gamma-chain receptor, 40 mM DMPC, 100 mM DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 15N, 13C, 85%2H Transmembrane domain of the Interleukin-7 receptor alpha subunit, 40 mM DMPC, 100 mM DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 15N, 2H Transmembrane domain of the common gamma-chain receptor, 0.4 mM 13C Transmembrane domain of the Interleukin-7 receptor alpha subunit, 40 mM deuterated DMPC (deuterated), 100 mM deuterated DH6PC (deuterated), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 15N, 2H Transmembrane domain of the Interleukin-7 receptor alpha subunit, 0.4 mM 13C Transmembrane domain of the common gamma-chain receptor, 40 mM deuterated DMPC (deuterated), 100 mM deuterated DH6PC (deuterated), 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 15N, 13C Transmembrane domain of the common gamma-chain receptor, 0.4 mM 15N, 13C Transmembrane domain of the Interleukin-7 receptor alpha subunit, 40 mM deuterated DMPC (deuterated), 100 mM deuterated DH6PC (deuterated), 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name IL7RA_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–223； UniProt 21–239

Cytokine receptor-like factor 2

Homo sapiens

UniProt Q9HC73

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 1–221 Not recorded Thymic stromal lymphopoietin × 1 （Q969D9） Interleukin-7 receptor subunit alpha × 1 （P16872） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.53 M ammonium sulfate 0.1 M sodium chloride 0.1 M BIS-TRIS pH 7.0 Resolution 3.55 Å R-free 0.225

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 5J12 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5J11 Structure of human TSLP in complex with TSLPR and IL-7Ralpha Deposited 2016-03-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–221（221 aa）
Mutation：N47Q PGE TRIETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；0.02 M Citric acid 0.08 M BIS-TRIS propane 16% w/v polyethylene glycol 3350
Resolution 2.56 Å R-free 0.218

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRLF2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–221； UniProt 1–221

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 5j12

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5j12
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5j12
Deposition date deposition_date2016-03-28
Structure title titleStructure of human TSLP:TSLPR in complex with mouse IL-7Ralpha
Keywords keywordscytokine inflammation TSLP signaling complex, signaling protein; SIGNALING PROTEIN
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_guinier28.08 Å
Radius of gyration Rg (electron density) rg_electron27.17 Å
Forward intensity I(0) i050390200.00
Molecular weight molecular_weight54142.0 kDa
Excluded volume excluded_volume67032 ų
Envelope volume envelope_volume87985 ų
Hydration-shell volume shell_volume27547 ų
Envelope diameter envelope_diameter96.0 Å
Shell Rg shell_rg33.84 Å
Envelope Rg envelope_rg27.33 Å
Shape Rg shape_rg27.18 Å
Total Rg total_rg27.83 Å
Total atoms total_atoms3814
Residues n_residues510
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 dmax90.6 Å
Rg (real space) rg_real28.06 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real5.0390e+07
I(0) uncertainty (real space) i0_real_error7.6390e+05
Rg (reciprocal space) rg_reciprocal28.07 Å
I(0) (reciprocal space) i0_reciprocal50390000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4 Å
Skewness Skewness skewness0.260
Kurtosis Kurtosis kurtosis-0.481
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6264000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.970
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5j12A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily90 — Thymic stromal lymphopoietin
Domain ID domain_id5j12B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1870 —
Domain ID domain_id5j12B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5j12C02
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)