Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit

The human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in the pathology of cancer, HIV, and COVID-19. Despite its significance as a drug target, the activation mechanism of CCR5, i.e. how chemokine agonists transduce the activation signal through the receptor, is yet unknown. Here, we report the cryo-EM structure of wild-type CCR5 in an active conformation bound to the chemokine super-agonist [6P4]CCL5 and the heterotrimeric Gi protein. The structure provides the rationale for the sequence-activity relation of agonist and antagonist chemokines. The N-terminus of agonist chemokines pushes onto an aromatic connector that transmits activation to the canonical GPCR microswitch network. This activation mechanism differs significantly from other CC chemokine receptors that bind shorter chemokines in a shallow binding mode and have unique sequence signatures and a specialized activation mechanism.One-sentence summaryThe structure of CCR5 in complex with the chemokine agonist [6P4]CCL5 and the heterotrimeric Gi protein reveals its activation mechanism

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“…The moderate outward displacement of TM6 and the arrangement of Gi relative to CCR5 (Fig. 1A-C) agrees with previous GPCR•Gi complexes (21,22).…”

Section: Overall Structure Of the [6p4]ccl5•ccr5•gi Complexsupporting

confidence: 91%

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

Isaikina

Tsai

Dietz

et al. 2020

Preprint

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“…Studies have suggested that the G βγ subunit of the G i -protein facilitates the coupling of the G αi subunit to the receptor, and the GDP/GTP exchange in the G αi subunit engenders the dissociation and interaction with downstream effectors, such as G αi inhibition of adenylyl cyclase and G βγ activation of ion channels 29,30 . Furthermore, recently solved structure of rhodopsin-G i complex clearly revealed that the interactions between rhodopsin and G i -protein are mainly mediated by the G αi subunit and somewhat by G βγ subunit 14,15,31 . Therefore, we only focused on a variation in the interaction pattern of G αi -protein with CXCR4 receptor to reduce the computing consumption in our systems.…”

Section: Resultsmentioning

confidence: 99%

“…Because the solved crystal structure of CXCR4 (PDB: 3ODU) lacks the N-terminus 4 , which is crucial in the initial binding of CXCL12 to CXCR4 6 , a full-length CXCR4 was constructed by attaching a missing N-terminus (a.a.: 1-26) obtained from the Protein Data Bank (PDB: 2N55) 17 to form a fully modeled CXCR4 containing 327 residues (a.a.: 1-327) according to the method proposed by Lei Xu, et al 7 . First, we superposed the NMR structures of the CXCR4 N-terminus with the CXCR4 N-terminal segment in the crystal structure (residues [27][28][29][30][31][32][33][34][35][36][37][38]. Then, the CXCR4 N-terminal segment (residues 27-38) in the NMR structure was deleted, and the best-oriented N-terminus (a.a.: 1-26) of CXCR4 from the NMR was attached manually to the crystal structure of CXCR4 using the Molecular Operating Environment (MOE) software package MOE2016.08 (http://www.chemcomp.com).…”

Section: Methodsmentioning

confidence: 99%

Internal water channel formation in CXCR4 is crucial for Gi-protein coupling upon activation by CXCL12

et al. 2020

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Chemokine receptor CXCR4 is a major drug target for numerous diseases because of its involvement in the regulation of cell migration and the developmental process. In this study, atomic-level molecular dynamics simulations were used to determine the activation mechanism and internal water formation of CXCR4 in complex with chemokine CXCL12 and Gi-protein. The results indicated that CXCL12-bound CXCR4 underwent transmembrane 6 (TM6) outward movement and a decrease in tyrosine toggle switch by eliciting the breakage of hydrophobic layer to form a continuous internal water channel. In the GDP-bound Gαi-protein state, the rotation and translation of the α5-helix of Gαi-protein toward the cytoplasmic pocket of CXCR4 induced an increase in interdomain distance for GDP leaving. Finally, an internal water channel formation model was proposed based on our simulations for CXCL12-bound CXCR4 in complex with Gαi-protein upon activation for downstream signaling. This model could be useful in anticancer drug development.

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“…This applies to the recognition of the ligands, but also for the recognition of the signaling transducers (G proteins and arrestins) to a given GPCR, which can be investigated by the same set of methods. How GPCRs select specific transducers remains enigmatic and cannot be firmly predicted from sequence or structural data alone [ 38 , 39 , 40 ]. Instead, the dynamic of the interactions and the existence several intermediate states may drive recognition and activation of the effector [ 19 , 41 , 42 ].…”

Section: Introductionmentioning

confidence: 99%

Capturing Peptide–GPCR Interactions and Their Dynamics

Kaiser

Coin

2020

Molecules

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Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.

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Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit

Cited by 59 publications

References 67 publications

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

Internal water channel formation in CXCR4 is crucial for Gi-protein coupling upon activation by CXCL12

Capturing Peptide–GPCR Interactions and Their Dynamics

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