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- PDB-8j3v: Structure of the transmembrane domain of human PD-L2 -

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Basic information

Entry
Database: PDB / ID: 8j3v
TitleStructure of the transmembrane domain of human PD-L2
ComponentsProgrammed cell death 1 ligand 2
KeywordsIMMUNE SYSTEM / PD-L2 / transmembrane domain / tumor / ligand
Function / homology
Function and homology information


negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / PD-1 signaling / endomembrane system / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / cellular response to lipopolysaccharide / adaptive immune response ...negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / PD-1 signaling / endomembrane system / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / cellular response to lipopolysaccharide / adaptive immune response / membrane => GO:0016020 / cell surface receptor signaling pathway / immune response / external side of plasma membrane / cell surface / signal transduction / extracellular region / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOuYang, B. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Deciphering Cholesterol's Role in PD-L2 Stability: A Distinct Regulatory Mechanism From PD-L1.
Authors: Zhang, Y. / Xiao, T. / Wen, M. / Shen, L. / Du, L. / Wei, S. / Wu, B. / Yu, Y. / Wang, S. / OuYang, B.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 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: Programmed cell death 1 ligand 2


Theoretical massNumber of molelcules
Total (without water)6,9361
Polymers6,9361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Programmed cell death 1 ligand 2


Mass: 6936.169 Da / Num. of mol.: 1 / Fragment: PD-L2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1LG2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQ51

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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 HSQC
122isotropic22D 1H-13C HSQC
133isotropic13D HNCO
143isotropic13D HNCA
153isotropic13D HN(CA)CO
163isotropic13D HN(CO)CA
173isotropic13D HN(CA)CB
182isotropic23D 1H-15N NOESY
192isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.5 mM [U-15N] PD-L2_TM, 90% H2O/10% D2O0.5 mM 15N-PD-L2-TM15N_PD-L2-TM90% H2O/10% D2O
bicelle20.5 mM [U-13C; U-15N] PD-L2_TM, 90% H2O/10% D2O13C-15N_PD-L2-TM90% H2O/10% D2O
bicelle30.5 mM [U-13C; U-15N; U-2H] PD-L2_TM, 90% H2O/10% D2O2H-13C-15N_PD-L2-TM90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPD-L2_TM[U-15N]1
0.5 mMPD-L2_TM[U-13C; U-15N]2
0.5 mMPD-L2_TM[U-13C; U-15N; U-2H]3
Sample conditionsDetails: 0.5 mM PD-L2-TM, 30 mM DMPC, 75 mM DHPC, 25 mM MES, pH 6.5
Ionic strength: 0 mM / Label: 30 mM DMPC, 75 mM DHPC, 25 mM MES, pH 6.5 / pH: 6.5 / Pressure: 0.1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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