2M2D

Human programmed cell death 1 receptor

Summary for 2M2D

• Entry DOI: 10.2210/pdb2m2d/pdb
• NMR Information: BMRB: 18908
• Descriptor: Programmed cell death protein 1 (1 entity in total)
• Functional Keywords: pd-1, apoptosis
• Biological source: Homo sapiens (human)
• Cellular location: Membrane; Single-pass type I membrane protein: Q15116
• Total number of polymer chains: 1
• Total formula weight: 13245.81

Authors

Veverka, V.,Cheng, X.,Waters, L.C.,Muskett, F.W.,Morgan, S.,Lesley, A.,Griffiths, M.,Stubberfield, C.,Griffin, R.,Henry, A.J.,Robinson, M.K.,Jansson, A.,Ladbury, J.E.,Ikemizu, S.,Davis, S.J.,Carr, M.D. (deposition date: 2012-12-18, release date: 2013-02-27, Last modification date: 2024-10-30)

Primary citation

Cheng, X.,Veverka, V.,Radhakrishnan, A.,Waters, L.C.,Muskett, F.W.,Morgan, S.H.,Huo, J.,Yu, C.,Evans, E.J.,Leslie, A.J.,Griffiths, M.,Stubberfield, C.,Griffin, R.,Henry, A.J.,Jansson, A.,Ladbury, J.E.,Ikemizu, S.,Carr, M.D.,Davis, S.J.
Structure and interactions of the human programmed cell death 1 receptor.
J.Biol.Chem., 288:11771-11785, 2013

PubMed Abstract: PD-1, a receptor expressed by T cells, B cells, and monocytes, is a potent regulator of immune responses and a promising therapeutic target. The structure and interactions of human PD-1 are, however, incompletely characterized. We present the solution nuclear magnetic resonance (NMR)-based structure of the human PD-1 extracellular region and detailed analyses of its interactions with its ligands, PD-L1 and PD-L2. PD-1 has typical immunoglobulin superfamily topology but differs at the edge of the GFCC' sheet, which is flexible and completely lacks a C" strand. Changes in PD-1 backbone NMR signals induced by ligand binding suggest that, whereas binding is centered on the GFCC' sheet, PD-1 is engaged by its two ligands differently and in ways incompletely explained by crystal structures of mouse PD-1 · ligand complexes. The affinities of these interactions and that of PD-L1 with the costimulatory protein B7-1, measured using surface plasmon resonance, are significantly weaker than expected. The 3-4-fold greater affinity of PD-L2 versus PD-L1 for human PD-1 is principally due to the 3-fold smaller dissociation rate for PD-L2 binding. Isothermal titration calorimetry revealed that the PD-1/PD-L1 interaction is entropically driven, whereas PD-1/PD-L2 binding has a large enthalpic component. Mathematical simulations based on the biophysical data and quantitative expression data suggest an unexpectedly limited contribution of PD-L2 to PD-1 ligation during interactions of activated T cells with antigen-presenting cells. These findings provide a rigorous structural and biophysical framework for interpreting the important functions of PD-1 and reveal that potent inhibitory signaling can be initiated by weakly interacting receptors.

PubMed: 23417675
DOI: 10.1074/jbc.M112.448126

Experimental method

SOLUTION NMR