Structure of the human Duffy antigen receptor

Saha, Shirsha; Khanppnavar, Basavraj; Maharana, Jagannath; Kim, H.R.; Carino, Carlo Marion C.; Daly, Carole; Houston, Shane; Kumari, Poonam; Yadav, Prem N.; Plouffe, Bianca; Inoue, Asuka; Chung, Ka Young; Banerjee, Rita; Korkhov, Volodymyr M.; Shukla, Arun K.

doi:10.1101/2023.07.09.548245

Cited by 2 publications

(6 citation statements)

References 87 publications

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“…Prior to grid freezing for high-resolution cryo-EM data collection, conventional uranyl-formate negative staining was used to assess sample homogeneity 79 18 . In brief, a formvar/carbon-coated 300 mesh copper grid (PELCO, Ted Pella) was dispensed with 3.5µl of the sample, incubated for 1 minute, and then blotted off using Whatman No.…”

Section: Methodsmentioning

confidence: 99%

“…Full length recombinant CXCR2/CXCR3 was isolated from Spodoptera frugiperda (Sf9) insect cells following a previously published protocol 18,69,86 . Sf9 cells were harvested 72h post-infection with CXCR2/CXCR3 expressing baculovirus.…”

Section: Methodsmentioning

confidence: 99%

“…While chemokine receptors exhibit a conserved seven transmembrane architecture characteristic of prototypical GPCRs, their interaction with chemokines does not always follow the exclusive natural agonist selectivity displayed by the majority of GPCRs 15 . This holds true for both C-C and C-X-C type chemokine receptors, as well as for atypical chemokine receptors, such as the Duffy antigen receptor for chemokines, which displays cross-reactivity across C-C and C-X-C chemokines [16][17][18] . Despite emerging structural insights into chemokine-recognition by chemokine receptors [19][20][21][22][23][24][25][26][27][28][29][30] , the molecular determinants underlying the inherent ligand promiscuity remain an enigma and represent an important knowledge gap in our current understanding of GPCR activation and signaling paradigm.…”

Section: Mainmentioning

confidence: 99%

“…Full length recombinant CXCR2/CXCR3 was isolated from Spodoptera frugiperda (Sf9) insect cells following a previously published protocol 18,69,86…”

Section: Purification Of Cxcr2 and Cxcr3mentioning

confidence: 99%

“…It is also striking that some of the C-C chemokine receptors maintain a high degree of ligand selectivity, for example, CCR9, similar to CXCR4 16,17 . In addition, some of the chemokine receptors such as the Duffy antigen receptor for chemokine (DARC), also known as the atypical chemokine receptor 1 (ACKR1), even displays cross-reactivity for C-C and C-X-C chemokines 18 . Therefore, the chemokine receptor subfamily represents a rich tapestry for future studies to uncover the fundamental principles that guide naturally encoded ligand-receptor pairing and signaling-bias at multiple levels.…”

Section: Mainmentioning

confidence: 99%

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Molecular basis of ligand promiscuity, structural mimicry, and atypical dimerization in the chemokine receptors

Saha,

Sano,

Sharma

et al. 2024

Preprint

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Selectivity of natural agonists for their cognate receptors is one of the hallmarks of the members of GPCR family, and it is crucial for the specificity of downstream signal-transduction. However, this selectivity often breaks down in the chemokine receptor subfamily, wherein a high degree of promiscuity is observed with one receptor recognizing multiple chemokines and one chemokine binding to multiple receptors. The molecular determinants of such a striking promiscuity for natural ligands in the chemokine-chemokine receptor system remain mostly elusive and represent an important knowledge gap in our current understanding. Here, we carry out a comprehensive transducer-coupling analysis, testing all known C-X-C chemokines on every C-X-C type chemokine receptor, to generate a global fingerprint of the selectivity and promiscuity encoded within this system. Taking lead from our finding, we determined cryo-EM structures of the most promiscuous receptor, CXCR2, in complex with every interacting chemokine, and deciphered the conserved molecular signatures and distinct binding modalities. While most chemokines position themselves on the receptor as a dimer, CXCL6 exhibits a monomeric binding pose induced by a previously unanticipated reorientation of its carboxyl-terminal α-helix, leading to disruption of the dimer interface. Surprisingly, one of the chemokines, CXCL5, induces a ligand-swapped dimer of CXCR2, the first of its kind observed in class A GPCRs, wherein each protomer of the ligand engages its own receptor without any discernible receptor-receptor interface. These unique observations provide a possible structural mechanism for inherent functional specialization encoded in chemokines despite their convergence to a common receptor. Furthermore, we also determined cryo-EM structures of CXCR3 in complex with G-protein-biased and β-arrestin-biased small molecule agonists that elucidate distinct allosteric modulations in the receptor driving their divergent transducer-coupling bias. Guided by structural analysis and experimental validation, we discover that in contrast to previously held notion, small molecule agonists of CXCR3 display robust agonism at CXCR7, an intrinsically biased, β-arrestin-coupled receptor, making them first-in-class dual agonists for chemokine receptors with exclusive βarr-bias at CXCR7. Taken together, our study provides molecular insights into ligand promiscuity and signaling bias at the chemokine receptors, and also demonstrates a proof of principle that naturally encoded structural mimicry can be recapitulated using synthetic pharmacophores with potential implications for developing novel therapeutics.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Mainmentioning

confidence: 99%

“…Full length recombinant CXCR2/CXCR3 was isolated from Spodoptera frugiperda (Sf9) insect cells following a previously published protocol 18,69,86…”

Section: Purification Of Cxcr2 and Cxcr3mentioning

confidence: 99%

Section: Mainmentioning

confidence: 99%

See 3 more Smart Citations

Molecular basis of ligand promiscuity, structural mimicry, and atypical dimerization in the chemokine receptors

Saha,

Sano,

Sharma

et al. 2024

Preprint

Self Cite

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Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

Kranjc,

Narwani,

Abby

et al. 2023

IJMS

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Plasmodium vivax malaria affects 14 million people each year. Its invasion requires interactions between the parasitic Duffy-binding protein (PvDBP) and the N-terminal extracellular domain (ECD1) of the host’s Duffy antigen/receptor for chemokines (DARC). ECD1 is highly flexible and intrinsically disordered, therefore it can adopt different conformations. We computationally modeled the challenging ECD1 local structure. With T-REMD simulations, we sampled its dynamic behavior and collected its most representative conformations. Our results suggest that most of the DARC ECD1 domain remains in a disordered state during the simulated time. Globular local conformations are found in the analyzed local free-energy minima. These globular conformations share an α-helix spanning residues Ser18 to Ser29 and in many cases they comprise an antiparallel β-sheet, whose β-strands are formed around residues Leu10 and Ala49. The formation of a parallel β-sheet is almost negligible. So far, progress in understanding the mechanisms forming the basis of the P. vivax malaria infection of reticulocytes has been hampered by experimental difficulties, along with a lack of DARC structural information. Our collection of the most probable ECD1 structural conformations will help to advance modeling of the DARC structure and to explore DARC–ECD1 interactions with a range of physiological and pathological ligands.

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Structure of the human Duffy antigen receptor

Cited by 2 publications

References 87 publications

Molecular basis of ligand promiscuity, structural mimicry, and atypical dimerization in the chemokine receptors

Molecular basis of ligand promiscuity, structural mimicry, and atypical dimerization in the chemokine receptors

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

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