6J15 image
Deposition Date 2018-12-27
Release Date 2019-11-06
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6J15
Keywords:
Title:
Complex structure of GY-5 Fab and PD-1
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Method Details:
Experimental Method:
Resolution:
2.60 Å
R-Value Free:
0.27
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Programmed cell death protein 1
Gene (Uniprot):PDCD1
Chain IDs:A (auth: C), B (auth: D)
Chain Length:120
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:GY-5 heavy chain Fab
Chain IDs:C (auth: H), E (auth: A)
Chain Length:219
Number of Molecules:2
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:GY-5 light chain Fab
Chain IDs:D (auth: L), F (auth: B)
Chain Length:216
Number of Molecules:2
Biological Source:Mus musculus
Ligand Molecules
Primary Citation
The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy.
Iscience 14 113 124 (2019)
PMID: 30952089 DOI: 10.1016/j.isci.2019.03.017

Abstact

Programmed cell death 1 (PD-1)/PD-1 ligand-1 (PD-L1)-blocking monoclonal antibodies (mAbs) have taken center stage for tumor immune checkpoint therapy. Identification of the "hotspots" on PD-1 for mAbs will help to develop next-generation oral deliverable agents with long-lasting efficacy. Here, we identified two PD-1-targeting mAbs, GY-5 and GY-14, with PD-1/PD-L1-blocking efficacy. Complex structural information revealed that both mAbs mainly bind to the FG loop of PD-1, which also contributes multiple interactions with PD-L1. The FG loop adopts substantially varied conformations upon binding to different mAbs, providing a novel targetable region for the development of PD-1-specific biologics and small chemical molecules. Glycosylation modifications of PD-1 could be observed in three of the four potential N-linked glycosylation sites. However, the binding of GY-5 and GY-14 to PD-1 was not affected by glycosylation. These findings broaden our understanding of the mechanism of anti-PD-1 mAbs and provide insight into the development of agents targeting PD-1.

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Primary Citation of related structures