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- PDB-8ddc: Intramembrane recognition between transmembrane domains of IL-7R ... -

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Basic information

Entry
Database: PDB / ID: 8ddc
TitleIntramembrane recognition between transmembrane domains of IL-7R and common gamma chain
Components
  • Cytokine receptor common subunit gamma
  • Interleukin-7 receptor subunit alpha
KeywordsMEMBRANE PROTEIN / common gamma-chain cytokine receptor / transmembrane domain / receptor sharing
Function / homology
Function and homology information


Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / interleukin-7 receptor activity / Interleukin-15 signaling / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / interleukin-7 receptor activity / Interleukin-15 signaling / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / Interleukin receptor SHC signaling / positive regulation of T cell differentiation in thymus / RAF/MAP kinase cascade / lymphocyte differentiation / positive regulation of receptor signaling pathway via STAT / interleukin-7-mediated signaling pathway / Cargo recognition for clathrin-mediated endocytosis / interleukin-9-mediated signaling pathway / Clathrin-mediated endocytosis / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / negative regulation of T cell apoptotic process / interleukin-15-mediated signaling pathway / cellular homeostasis / positive regulation of B cell differentiation / regulation of cell size / T cell homeostasis / B cell homeostasis / B cell proliferation / T cell differentiation / lymph node development / coreceptor activity / positive regulation of phagocytosis / B cell differentiation / T cell mediated cytotoxicity / cell morphogenesis / T cell differentiation in thymus / regulation of gene expression / gene expression / defense response to Gram-positive bacterium / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. ...IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-7 receptor subunit alpha / Cytokine receptor common subunit gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsCai, T. / Lenoir Capello, R. / Chou, J.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140887 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150709 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM132079 United States
CitationJournal: Science / Year: 2023
Title: Structural basis of gamma chain family receptor sharing at the membrane level.
Authors: Cai, T. / Lenoir Capello, R. / Pi, X. / Wu, H. / Chou, J.J.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokine receptor common subunit gamma
B: Interleukin-7 receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)7,3172
Polymers7,3172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, Inter-molecular NOEs
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1000 Å2
ΔGint-12 kcal/mol
Surface area6190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / ...Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / gammaC / p64


Mass: 3864.547 Da / Num. of mol.: 1 / Fragment: Transmembrane domain, residues 253-286 / Mutation: M271V, C282F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il2rg / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34902
#2: Protein/peptide Interleukin-7 receptor subunit alpha / IL-7 receptor subunit alpha / IL-7R subunit alpha / IL-7R-alpha / IL-7RA


Mass: 3452.199 Da / Num. of mol.: 1 / Fragment: Transmembrane domain, residues 236-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il7r / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16872

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY-HSQC
122isotropic12D 1H-15N TROSY-HSQC
133isotropic52D 1H-15N TROSY-HSQC
144isotropic52D 1H-15N TROSY-HSQC
153isotropic42D 1H-13C HSQC
164isotropic42D 1H-13C HSQC
171isotropic13D TROSY HNCA
182isotropic13D TROSY HNCA
191isotropic13D TROSY HN(CO)CA
1102isotropic13D TROSY HN(CO)CA
1111isotropic13D TROSY HNCO
1122isotropic13D TROSY HNCO
1131isotropic13D TROSY HN(CA)CO
1142isotropic13D TROSY HN(CA)CO
1153isotropic53D 1H-15N NOESY-TROSY
1164isotropic53D 1H-15N NOESY-TROSY
1175isotropic43D 1H-15N NOESY-TROSY
1183isotropic33D 1H-13C NOESY
1194isotropic33D 1H-13C NOESY
1215isotropic43D 1H-13C NOESY
1203isotropic32D Methyl-Amide Intermolecular NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.4 mM 15N, 13C, 85%2H Transmembrane domain of the common gamma-chain receptor, 40 mM DMPC, 100 mM DH6PC, 90% H2O/10% D2O(15N,13C,85%2H)-labeled gamma-chain TMD in DMPC-DHPC bicelles (q=0.4) for triple-resonance experiments.gC(15N,13C,85%2H)90% H2O/10% D2O
bicelle20.4 mM 15N, 13C, 85%2H Transmembrane domain of the Interleukin-7 receptor alpha subunit, 40 mM DMPC, 100 mM DH6PC, 90% H2O/10% D2O(15N,13C,85%2H)-labeled IL-7 receptor TMD in DMPC-DHPC bicelles (q=0.4) for triple-resonance experiments.7R(15N,13C,85%2H)90% H2O/10% D2O
bicelle30.4 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(15N,2H)-labeled gamma chain TMD mixed with (13C)-labeled IL-7 receptor TMD at 1:1 molar ratio in DMPC-DHPC bicelles (q=0.4), for detecting inter-molecular NOEs.gC(15N,2H)-7R(13C)90% H2O/10% D2O
bicelle40.4 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(15N,2H)-labeled IL-7 receptor TMD mixed with (13C)-labeled gamma chain TMD at 1:1 molar ratio in DMPC-DHPC bicelles (q=0.4), for detecting inter-molecular NOEs.7R(15N,2H)-gC(13C)90% H2O/10% D2O
bicelle50.4 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(15N,13C)-labeled gamma chain TMD mixed with (15N,13C)-labeled IL-7 receptor TMD at 1:1 molar ratio in deuterated DMPC-DHPC bicelles (q=0.4), for regular NOE experimentsgC(15N,13C)-7R(15N,13C)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMTransmembrane domain of the common gamma-chain receptor15N, 13C, 85%2H1
40 mMDMPCnatural abundance1
100 mMDH6PCnatural abundance1
0.4 mMTransmembrane domain of the Interleukin-7 receptor alpha subunit15N, 13C, 85%2H2
40 mMDMPCnatural abundance2
100 mMDH6PCnatural abundance2
0.4 mMTransmembrane domain of the common gamma-chain receptor15N, 2H3
0.4 mMTransmembrane domain of the Interleukin-7 receptor alpha subunit13C3
40 mMDMPC (deuterated)deuterated3
100 mMDH6PC (deuterated)deuterated3
0.4 mMTransmembrane domain of the Interleukin-7 receptor alpha subunit15N, 2H4
0.4 mMTransmembrane domain of the common gamma-chain receptor13C4
40 mMDMPC (deuterated)deuterated4
100 mMDH6PC (deuterated)deuterated4
0.4 mMTransmembrane domain of the common gamma-chain receptor15N, 13C5
0.4 mMTransmembrane domain of the Interleukin-7 receptor alpha subunit15N, 13C5
40 mMDMPC (deuterated)deuterated5
100 mMDH6PC (deuterated)deuterated5
Sample conditionsDetails: The condition used for all NMR data collection / Ionic strength: 0.15 M / Label: NMR measurements / pH: 6.7 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 303 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE NEOBrukerAVANCE NEO7003
Bruker AVANCE IIIBrukerAVANCE III8004
Bruker AVANCE IIIBrukerAVANCE III9005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
TALOS+Shen, Delaglio, Cornilescu, Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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