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8ddc

Intramembrane recognition between transmembrane domains of IL-7R and common gamma chain

Method: SOLUTION NMR Dmax: 68.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytokine receptor common subunit gamma

Mus musculus

UniProt P34902

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 253–286 Fragment：Transmembrane domain, residues 253-286 Mutation：M271V, C282F Interleukin-7 receptor subunit alpha × 1 （P16872） 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

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 8DDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6DG5 Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg Deposited 2018-05-16 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 C 56–254（199 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.091 M Tris pH 7.5 8 mM imidazole pH 8.0 4.2% DEXTRAN SULFATE 50 mM sodium citrate 2.2 M ammonium sulfate
Resolution 2.52 Å R-free 0.266
8DDD Intramembrane recognition between transmembrane domains of IL-9R and common gamma chain Deposited 2022-06-17 Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 253–286（34 aa） Fragment：Transmembrane domain, residues 253-286
Mutation：M271V, C282F 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-9 receptor alpha subunit, 40 mM DMPC, 100 mM DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 13C Transmembrane domain of the Interleukin-9 receptor alpha subunit, 0.4 mM 15N, 2H Transmembrane domain of the common gamma-chain receptor, 80 mM deuterated DMPC, 200 mM deuterated DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 13C Transmembrane domain of the common gamma-chain receptor, 0.4 mM 15N, 2H Transmembrane domain of the Interleukin-9 receptor alpha subunit, 80 mM deuterated DMPC, 200 mM deuterated DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4 mM 13C Transmembrane domain of the Interleukin-9 receptor alpha subunit, 0.4 mM 15N, 2H Transmembrane domain of the common gamma-chain receptor, 80 mM deuterated DMPC, 200 mM deuterated DH6PC, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

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

View Construct and Data Evidence
UniProt name IL2RG_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–34； UniProt 253–286

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 236–266 Fragment：Transmembrane domain, residues 236-266 Cytokine receptor common subunit gamma × 1 （P34902） 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

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 8DDC 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 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 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 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 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

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 1–31； UniProt 236–266

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 8ddc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ddc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ddc
Deposition date deposition_date2022-06-17
Structure title titleIntramembrane recognition between transmembrane domains of IL-7R and common gamma chain
Keywords keywordscommon gamma-chain cytokine receptor, transmembrane domain, receptor sharing, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.71 Å
Radius of gyration Rg (electron density) rg_electron16.82 Å
Forward intensity I(0) i0109718000.00
Molecular weight molecular_weight109660.0 kDa
Excluded volume excluded_volume146170 ų
Envelope volume envelope_volume32551 ų
Hydration-shell volume shell_volume13515 ų
Envelope diameter envelope_diameter72.9 Å
Shell Rg shell_rg26.78 Å
Envelope Rg envelope_rg22.69 Å
Shape Rg shape_rg16.88 Å
Total Rg total_rg17.00 Å
Total atoms total_atoms16140
Residues n_residues975
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 dmax68.0 Å
Rg (real space) rg_real18.00 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real1.0970e+08
I(0) uncertainty (real space) i0_real_error1.8150e+06
Rg (reciprocal space) rg_reciprocal17.96 Å
I(0) (reciprocal space) i0_reciprocal109700000.0000
Solution quality estimate total_estimate0.6715
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary14.5 Å
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.521
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29310.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.201; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.135; Smooth: 0.993
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)