Qing Fan: Inside the Architecture of Class C GPCRs

Class C GPCRs are structural and mechanistic outliers within the GPCR superfamily. Unlike class A receptors, which bind orthosteric ligands within their transmembrane domain and can function as monomers, class C receptors carry an additional extracellular domain of 500 to 600 amino acids that houses the agonist binding site - and they require dimerization as a prerequisite for function. Despite the clinical significance of their members, particularly the GABA-B receptor, the metabotropic glutamate receptors, and the calcium-sensing receptor, the molecular mechanisms governing their activation and regulation remain incompletely understood.

Fan's laboratory at Columbia University has spent more than a decade investigating the three-dimensional architecture of the GABA-B receptor - the first known obligatory GPCR heterodimer - across multiple functional states. Her work has produced structural data at the extracellular domain level and, more recently, full-length cryo-EM structures in inactive conformation, leading to an unexpected discovery: phospholipids embedded inside each transmembrane bundle that appear to function as both structural anchors and negative allosteric modulators.

This conversation covers the current structural landscape of class C GPCRs, how genetic disease mutations in the transmembrane domain connect to Rett syndrome and epileptic encephalopathy, and what allosteric and biased signaling strategies could offer that baclofen - the only FDA-approved GABA-B drug - cannot. Fan's commitment to this receptor began with a single structural observation during her postdoc: dimers forming in an FSH receptor crystal that she could not set aside.

ABOUT THE GUEST

Qing Fan is an associate professor of pharmacology and pathology and cell biology at Columbia University. A structural biologist by training, her research focuses on the three-dimensional architecture of class C GPCRs - with particular emphasis on the GABA-B receptor, which she has studied as her primary independent research question for over a decade. Her work employs X-ray crystallography, single-particle cryo-EM, mutagenesis, and mass spectrometry, often through cross-disciplinary collaboration, to connect structural findings to receptor function and disease-relevant biology. Fan's structural studies of the full-length GABA-B receptor contributed to a wave of publications that, in the same year, established inactive, active, and intermediate conformational states of this receptor using cryo-EM.

SCIENTIFIC THEMES OF THE CONVERSATION

• The structural architecture that sets class C GPCRs apart from class A - and why that architecture makes activation harder to study
  

• Obligate heterodimerization as a functional requirement, not a regulatory option
  

• The unexpected discovery of embedded phospholipids inside the GABA-B transmembrane bundle and their role as structural and allosteric components
  

• Disease-associated mutations in the GABA-B transmembrane domain and what they suggest about precision pharmacology
  

• The therapeutic landscape of GABA-B: baclofen's limitations and the case for allosteric and biased approaches
  

• Cryo-EM as a catalyst for structural pharmacology - what it enabled and what it still cannot resolve

KEY INSIGHTS FROM THE CONVERSATION

Class C GPCRs carry a fundamentally different activation logic In class A receptors, the orthosteric ligand binds inside the transmembrane bundle and directly induces conformational changes that activate the receptor. In class C receptors, the orthosteric site sits inside a large extracellular domain that is physically remote from the transmembrane core. How the agonist binding event at the extracellular level is communicated downward to activate the transmembrane domain remains an open mechanistic question - and it is the central problem Fan's laboratory is trying to answer.

Dimerization is not optional - it is the mechanism GABA-B is an obligate heterodimer: the GABA-B1 subunit carries the agonist binding site; the GABA-B2 subunit is required for trafficking to the cell surface and for G protein coupling. Neither subunit functions without the other. Fan's structural work identified a quartet of charged residues - salt bridges between TM3 and TM5 helices of both subunits - that she terms the inter-subunit latch. Disrupting this latch through mutagenesis produces constitutive receptor activity, suggesting it is a critical component of the receptor's inactive state.

Phospholipids inside the transmembrane bundle: a discovery nobody expected When Fan's team solved the full-length cryo-EM structure of inactive GABA-B, they found a bulky phospholipid occupying the internal cavity of each TM bundle. Using mass spectrometry in collaboration with colleagues at UC Davis, they identified the exact molecular identity of both lipids and assigned one to each subunit based on head group size differences. Both lipids form extensive contacts with their respective subunits, leading Fan to propose they are necessary structural components - not incidental contaminants. Mutational analysis of the GABA-B2-bound lipid site further suggested that lipid acts as a negative allosteric modulator, though Fan is careful to note that more thorough characterization is needed before conclusions can be drawn about each lipid's specific functional role.

Rett syndrome and epilepsy mutations point directly to the transmembrane domain Single amino acid mutations in GABA-B2 have been linked to Rett syndrome and epileptic encephalopathy. These mutations map to the transmembrane domain - the same region where Fan's team identified the embedded lipid binding site. The proximity raises the question of whether some disease mutations exert their effects by disrupting lipid-receptor interactions. Fan describes the resolve-the-disease-isoform-structure approach as underutilized: most structural work focuses on wild-type receptors, while patients with genetic disease are born with receptors that may behave very differently - and that may respond differently to existing drugs.

Baclofen works. But its therapeutic window is narrow. Baclofen, a selective GABA-B agonist, is the only FDA-approved drug targeting this receptor. It is used to treat muscle spasticity in multiple sclerosis and spinal cord injury, but it carries significant side effects - including drowsiness and weakness - that limit its clinical utility. Fan describes the allosteric sites within the transmembrane domain as a more targeted alternative: they offer receptor modulation without directly competing with the endogenous agonist at the orthosteric site, and they map onto the same transmembrane region where disease-relevant mutations cluster.

The biased agonism framework still offers real specificity - if applied carefully Fan points to the 2016 work on the mu opioid receptor by Kobilka, Gnäder, Roth, and Shokat as an illustration of what pathway-selective drug design can achieve: a compound that confers analgesia through G protein signaling while avoiding the respiratory depression associated with beta-arrestin pathway activation. She acknowledges the field's more recent reassessment of how clean that selectivity actually is in vivo - but holds that the underlying principle of fine-tuning rather than binary pathway switching remains a viable and underexplored pharmacological strategy for GPCR-targeted drug design.

A decade on one receptor: the cost and the clarity it produces Fan has worked on the GABA-B receptor since it became her first independent project. Over more than ten years, the questions have deepened rather than resolved: the lipid finding opened new lines of inquiry; the disease mutation connections raised new structural puzzles; the cryo-EM structures raised as many mechanistic questions as they answered. Her description of this trajectory is not frustration - it is the argument for sustained focus. The field has moved from not knowing the subunit composition of GABA-B to holding cryo-EM structures in inactive, active, and intermediate states. That arc is the product of a community of researchers willing to stay with one system long enough to see it clearly.

EPISODE TIMELINE

Timestamps are AI-generated approximations based on transcript markers and may not reflect exact positions in the final edited video.

• 00:00 - Opening announcements

• 01:26 - Fan's background as a structural biologist and path to class C GPCRs

• 04:39 - Why class C GPCRs remain the less-explored side of the GPCR superfamily

• 05:11 - The architecture of GABA-B: extracellular domains, obligate heterodimerization, and field milestones since the 1970s

• 11:02 - The unexpected cryo-EM finding: phospholipids embedded inside each transmembrane bundle

• 12:55 - What the lipids actually do - structural components, allosteric modulation, and open questions

• 14:57 - Disease territory: epilepsy, spasticity, pain, addiction, and the limitations of baclofen

• 16:17 - The case for resolving disease isoform structures as a path toward precision medicine

• 19:03 - GPCRs as drug targets: allosteric sites, biased signaling, and what the mu opioid receptor example demonstrated

• 23:37 - What full-length structures in multiple states still need to deliver for drug design

• 25:01 - Advice for early-career scientists: the role of passion in sustained scientific work

• 26:15 - Three "aha" moments that shaped a career - from MHC antigen presentation to the cryo-EM revolution

• 29:55 - Increasing diversity in science through mentorship, structured Q&A, and institutional commitment

SELECTED QUOTES

About this episode

Dr. Fan is currently an associate professor of Pharmacology and Pathology and Cell Biology at Columbia University in NYC. Qing is a structural biologist interested in the molecular mechanisms controlling how class C GPCRs transmit signals. She obtained her bachelor's, master and doctoral degrees at Harvard University and completed her postdoctoral training with Dr. Hendrickson at Columbia University.

Join us and learn more about Qing's work and how we powered through a technical issue during the interview.

Dr. Qing Fan on the web

• Fan Lab

• Dr. Fan at Columbia University

• Research Gate

• LinkedIn

• Pubmed

• Dr. GPCR Ecosystem