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4nn5

Cytokine receptor complex - Crystal form 1A

Method: X-RAY DIFFRACTION Dmax: 93.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thymic stromal lymphopoietin

Mus musculus

UniProt Q9JIE6

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 20–140 Fragment：UNP residues 20-140 Mutation：N123Q Interleukin-7 receptor subunit alpha × 1 （P16872） Cytokine receptor-like factor 2 × 1 （Q8CII9） 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

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 4NN5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NN6 Cytokine receptor complex - Crystal form 1B Deposited 2013-11-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–140（121 aa） Fragment：UNP residues 20-140
Mutation：N123Q 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–140（121 aa） Fragment：UNP residues 20-140
Mutation：N123Q 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

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

View Construct and Data Evidence
UniProt name TSLP_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–121； UniProt 20–140

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 Fragment：extracellular domain (UNP residues 21-239) Thymic stromal lymphopoietin × 1 （Q9JIE6） Cytokine receptor-like factor 2 × 1 （Q8CII9） 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

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 4NN5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NN6 Cytokine receptor complex - Crystal form 1B Deposited 2013-11-16 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 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
5J12 Structure of human TSLP:TSLPR in complex with mouse IL-7Ralpha Deposited 2016-03-28 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）
Not recorded 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
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

Mus musculus

UniProt Q8CII9

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 20–222 Fragment：extracellular domain (UNP residues 20-222) Mutation：N122Q Thymic stromal lymphopoietin × 1 （Q9JIE6） Interleukin-7 receptor subunit alpha × 1 （P16872） 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

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 4NN5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NN6 Cytokine receptor complex - Crystal form 1B Deposited 2013-11-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 20–222（203 aa） Fragment：extracellular domain (UNP residues 20-222)
Mutation：N122Q 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 20–222（203 aa） Fragment：extracellular domain (UNP residues 20-222)
Mutation：N53Q 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

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

View Construct and Data Evidence
UniProt name CRLF2_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–203； UniProt 20–222

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 4nn5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4nn5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4nn5
Deposition date deposition_date2013-11-16
Structure title titleCytokine receptor complex - Crystal form 1A
Keywords keywords;four helical bundle fold, CHR domains, TSLP cytokine signaling, TSLPR and IL-7Ralpha receptors, cell surface, 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_guinier27.87 Å
Radius of gyration Rg (electron density) rg_electron27.11 Å
Forward intensity I(0) i047546200.00
Molecular weight molecular_weight54262.0 kDa
Excluded volume excluded_volume68065 ų
Envelope volume envelope_volume85835 ų
Hydration-shell volume shell_volume26900 ų
Envelope diameter envelope_diameter96.5 Å
Shell Rg shell_rg33.74 Å
Envelope Rg envelope_rg27.21 Å
Shape Rg shape_rg27.07 Å
Total Rg total_rg27.92 Å
Total atoms total_atoms7523
Residues n_residues489
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 dmax93.4 Å
Rg (real space) rg_real27.84 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real4.7550e+07
I(0) uncertainty (real space) i0_real_error7.1560e+05
Rg (reciprocal space) rg_reciprocal27.85 Å
I(0) (reciprocal space) i0_reciprocal47550000.0000
Solution quality estimate total_estimate0.8965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.4 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.501
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6300000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.986
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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) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id4nn5A00
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_id4nn5B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1870 —
Domain ID domain_id4nn5B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4nn5C01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4nn5C02
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)