8J3V | pdb_00008j3v

Structure of the transmembrane domain of human PD-L2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 8J3V

This is version 1.1 of the entry. See complete history

Literature

Deciphering Cholesterol's Role in PD-L2 Stability: A Distinct Regulatory Mechanism From PD-L1.

Zhang, Y.Xiao, T.Wen, M.Shen, L.Du, L.Wei, S.Wu, B.Yu, Y.Wang, S.OuYang, B.

(2024) J Mol Biology 436: 168500-168500

  • DOI: https://doi.org/10.1016/j.jmb.2024.168500
  • Primary Citation Related Structures: 
    8J3V

  • PubMed Abstract: 

    Programmed cell death 1 ligand 2 (PD-L2), a member of the B7 immune checkpoint protein family, emerges as a crucial player in immune modulation. Despite its functional overlap with programmed cell death 1 ligand 1 (PD-L1) in binding to the programmed cell death protein 1 (PD-1) on T cells, PD-L2 exhibits a divergent expression pattern and a higher affinity for PD-1. However, the regulatory mechanisms of PD-L2 remain under-explored. Here, our investigations illustrate the pivotal role of cholesterol in modulating PD-L2 stability. Using advanced nuclear magnetic resonance (NMR) and biochemical analyses, we demonstrate a direct and specific binding between cholesterol and PD-L2, mediated by an F-xxx-V-xx-LR motif in its transmembrane domain, distinct from that in PD-L1. This interaction stabilizes PD-L2 and prevents its downstream degradation. Disruption of this binding motif compromises PD-L2's cellular stability, underscoring its potential significance in cancer biology. These findings not only deepen our understanding of PD-L2 regulation in the context of tumors, but also open avenues for potential therapeutic interventions.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecule Content 

  • Total Structure Weight: 6.94 kDa 
  • Atom Count: 491 
  • Modeled Residue Count: 60 
  • Deposited Residue Count: 60 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 260Homo sapiensMutation(s): 0 
Gene Names: PDCD1LG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ51 (Homo sapiens)
Explore Q9BQ51 
Go to UniProtKB:  Q9BQ51
PHAROS:  Q9BQ51
GTEx:  ENSG00000197646 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQ51
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references