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Agonist-bound structure of the human P2Y12 receptor.

Zhang J, Zhang K, Gao ZG, Paoletta S, Zhang D, Han GW, Li T, Ma L, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q - Nature (2014)

Bottom Line: Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets.The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding.As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

View Article: PubMed Central - PubMed

Affiliation: 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2].

ABSTRACT
The P2Y12 receptor (P2Y12R), one of eight members of the P2YR family expressed in humans, is one of the most prominent clinical drug targets for inhibition of platelet aggregation. Although mutagenesis and modelling studies of the P2Y12R provided useful insights into ligand binding, the agonist and antagonist recognition and function at the P2Y12R remain poorly understood at the molecular level. Here we report the structures of the human P2Y12R in complex with the full agonist 2-methylthio-adenosine-5'-diphosphate (2MeSADP, a close analogue of endogenous agonist ADP) at 2.5 Å resolution, and the corresponding ATP derivative 2-methylthio-adenosine-5'-triphosphate (2MeSATP) at 3.1 Å resolution. These structures, together with the structure of the P2Y12R with antagonist ethyl 6-(4-((benzylsulfonyl)carbamoyl)piperidin-1-yl)-5-cyano-2-methylnicotinate (AZD1283), reveal striking conformational changes between nucleotide and non-nucleotide ligand complexes in the extracellular regions. Further analysis of these changes provides insight into a distinct ligand binding landscape in the δ-group of class A G-protein-coupled receptors (GPCRs). Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets. The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding. As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

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Crystal packing of P2Y12R-2MeSADP, P2Y12R-2MeSATP and P2Y12R-AZD1283 complexes. (a) Overall structure of the P2Y12R-2MeSADP complex, P2Y12R and BRIL are shown in cyan and blue, respectively. (b and c) Crystal packing of P2Y12R-2MeSADP complex at two different views. (d) Overall structure of the P2Y12R-2MeSATP complex, P2Y12R is shown in pink. (e and f) Crystal packing of P2Y12R-2MeSATP complex at two different views. (g) Overall structure of the P2Y12R-AZD1283 complex, P2Y12R is shown in orange. (h and i) Crystal packing of P2Y12R-AZD1283 complex at two different views.
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Figure 6: Crystal packing of P2Y12R-2MeSADP, P2Y12R-2MeSATP and P2Y12R-AZD1283 complexes. (a) Overall structure of the P2Y12R-2MeSADP complex, P2Y12R and BRIL are shown in cyan and blue, respectively. (b and c) Crystal packing of P2Y12R-2MeSADP complex at two different views. (d) Overall structure of the P2Y12R-2MeSATP complex, P2Y12R is shown in pink. (e and f) Crystal packing of P2Y12R-2MeSATP complex at two different views. (g) Overall structure of the P2Y12R-AZD1283 complex, P2Y12R is shown in orange. (h and i) Crystal packing of P2Y12R-AZD1283 complex at two different views.

Mentions: The receptor is folded into a canonical seven transmembrane (7TM) bundle with a partially resolved intracellular helix VIII (Fig. 1). The straight conformation and tilted orientation of helix V observed in the AZD1283-bound structure5, is likely a genuine structural feature inherent to the P2Y12R as it is consistent in all three structures despite the different crystal packing configurations (Extended Data Fig. 2). Both the disulfide bonds, bridging the N-terminus (C17) with helix VII (C2707.25, superscript indicates Ballesteros-Weinstein residue numbering18) and the highly conserved disulfide bond between helix III (C973.25) and extracellular loop 2 (ECL2, C175) are observed.


Agonist-bound structure of the human P2Y12 receptor.

Zhang J, Zhang K, Gao ZG, Paoletta S, Zhang D, Han GW, Li T, Ma L, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, Zhao Q - Nature (2014)

Crystal packing of P2Y12R-2MeSADP, P2Y12R-2MeSATP and P2Y12R-AZD1283 complexes. (a) Overall structure of the P2Y12R-2MeSADP complex, P2Y12R and BRIL are shown in cyan and blue, respectively. (b and c) Crystal packing of P2Y12R-2MeSADP complex at two different views. (d) Overall structure of the P2Y12R-2MeSATP complex, P2Y12R is shown in pink. (e and f) Crystal packing of P2Y12R-2MeSATP complex at two different views. (g) Overall structure of the P2Y12R-AZD1283 complex, P2Y12R is shown in orange. (h and i) Crystal packing of P2Y12R-AZD1283 complex at two different views.
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Related In: Results  -  Collection

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Figure 6: Crystal packing of P2Y12R-2MeSADP, P2Y12R-2MeSATP and P2Y12R-AZD1283 complexes. (a) Overall structure of the P2Y12R-2MeSADP complex, P2Y12R and BRIL are shown in cyan and blue, respectively. (b and c) Crystal packing of P2Y12R-2MeSADP complex at two different views. (d) Overall structure of the P2Y12R-2MeSATP complex, P2Y12R is shown in pink. (e and f) Crystal packing of P2Y12R-2MeSATP complex at two different views. (g) Overall structure of the P2Y12R-AZD1283 complex, P2Y12R is shown in orange. (h and i) Crystal packing of P2Y12R-AZD1283 complex at two different views.
Mentions: The receptor is folded into a canonical seven transmembrane (7TM) bundle with a partially resolved intracellular helix VIII (Fig. 1). The straight conformation and tilted orientation of helix V observed in the AZD1283-bound structure5, is likely a genuine structural feature inherent to the P2Y12R as it is consistent in all three structures despite the different crystal packing configurations (Extended Data Fig. 2). Both the disulfide bonds, bridging the N-terminus (C17) with helix VII (C2707.25, superscript indicates Ballesteros-Weinstein residue numbering18) and the highly conserved disulfide bond between helix III (C973.25) and extracellular loop 2 (ECL2, C175) are observed.

Bottom Line: Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets.The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding.As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

View Article: PubMed Central - PubMed

Affiliation: 1] CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China [2].

ABSTRACT
The P2Y12 receptor (P2Y12R), one of eight members of the P2YR family expressed in humans, is one of the most prominent clinical drug targets for inhibition of platelet aggregation. Although mutagenesis and modelling studies of the P2Y12R provided useful insights into ligand binding, the agonist and antagonist recognition and function at the P2Y12R remain poorly understood at the molecular level. Here we report the structures of the human P2Y12R in complex with the full agonist 2-methylthio-adenosine-5'-diphosphate (2MeSADP, a close analogue of endogenous agonist ADP) at 2.5 Å resolution, and the corresponding ATP derivative 2-methylthio-adenosine-5'-triphosphate (2MeSATP) at 3.1 Å resolution. These structures, together with the structure of the P2Y12R with antagonist ethyl 6-(4-((benzylsulfonyl)carbamoyl)piperidin-1-yl)-5-cyano-2-methylnicotinate (AZD1283), reveal striking conformational changes between nucleotide and non-nucleotide ligand complexes in the extracellular regions. Further analysis of these changes provides insight into a distinct ligand binding landscape in the δ-group of class A G-protein-coupled receptors (GPCRs). Agonist and non-nucleotide antagonist adopt different orientations in the P2Y12R, with only partially overlapped binding pockets. The agonist-bound P2Y12R structure answers long-standing questions surrounding P2Y12R-agonist recognition, and reveals interactions with several residues that had not been reported to be involved in agonist binding. As a first example, to our knowledge, of a GPCR in which agonist access to the binding pocket requires large-scale rearrangements in the highly malleable extracellular region, the structural and docking studies will therefore provide invaluable insight into the pharmacology and mechanisms of action of agonists and different classes of antagonists for the P2Y12R and potentially for other closely related P2YRs.

Show MeSH
Related in: MedlinePlus