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 6L8R | pdb_00006l8r

membrane-bound PD-L1-CD


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6L8R

This is version 1.4 of the entry. See complete history. 

Literature

PD-L1 degradation is regulated by electrostatic membrane association of its cytoplasmic domain.

Wen, M., Cao, Y., Wu, B., Xiao, T., Cao, R., Wang, Q., Liu, X., Xue, H., Yu, Y., Lin, J., Xu, C., Xu, J., OuYang, B.

(2021) Nat Commun 12: 5106-5106

  • DOI: https://doi.org/10.1038/s41467-021-25416-7
  • Primary Citation Related Structures: 
    6L8R

  • PubMed Abstract: 

    The cytoplasmic domain of PD-L1 (PD-L1-CD) regulates PD-L1 degradation and stability through various mechanism, making it an attractive target for blocking PD-L1-related cancer signaling. Here, by using NMR and biochemical techniques we find that the membrane association of PD-L1-CD is mediated by electrostatic interactions between acidic phospholipids and basic residues in the N-terminal region. The absence of the acidic phospholipids and replacement of the basic residues with acidic residues abolish the membrane association. Moreover, the basic-to-acidic mutations also decrease the cellular abundance of PD-L1, implicating that the electrostatic interaction with the plasma membrane mediates the cellular levels of PD-L1. Interestingly, distinct from its reported function as an activator of AMPK in tumor cells, the type 2 diabetes drug metformin enhances the membrane dissociation of PD-L1-CD by disrupting the electrostatic interaction, thereby decreasing the cellular abundance of PD-L1. Collectively, our study reveals an unusual regulatory mechanism that controls the PD-L1 level in tumor cells, suggesting an alternative strategy to improve the efficacy of PD-L1-related immunotherapies.


  • 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, China. mrwen@sibcb.ac.cn.

Macromolecule Content 

  • Total Structure Weight: 3.8 kDa 
  • Atom Count: 262 
  • Modeled Residue Count: 33 
  • Deposited Residue Count: 33 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 133Homo sapiensMutation(s): 0 
Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens)
Explore Q9NZQ7 
Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7
GTEx:  ENSG00000120217 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31861133009

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Structure summary
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references