Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE

Abstract

SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport.

Substrate Binding and Inhibition of the Anion Exchanger 1 Transporter

“…Overall, our structures conform with known SLC4 architecture; two AE1 protomers form a homodimeric complex (Fig 1). However, unlike previous SLC4 transporter structures 11–13 , our full-length AE1 reconstruction reveals the relative orientation of cdAE1 and mdAE1 (Fig 1, Extended Data Figure 1C). In our resulting model cdAE1 orients perpendicular to mdAE1.…”

“…Compared to previous work, our studies reveal a fully ordered extracellular surface, including all Diego blood group antigens and glycosylation sites. This observation is surprising as AE1’s extracellular surface does not contain secondary structure elements compared to e.g., NDCBE (SLC4A8) 13 . We also reveal several bound lipids and sterols, whose effects on AE1 structure and function have been heavily speculated on 19,27,28 .…”

Intracellular pH Control by Membrane Transport in Mammalian Cells. Insights Into the Selective Advantages of Functional Redundancy

“…The interested readers can find the cryoEM structures of the Sodium-driven Chloride/Bicarbonate Exchanger NDCBE (SLC4A8) in (Wang et al, 2021), of the electrogenic sodiumbicarbonate cotransporter structure in (Huynh et al, 2018), and 1. The model also encompasses the electrogenic pumps and the passive channels that set the membrane potential (Em) and also use the same substrates as the coupling anions and cations that energize some of the pH regulatory transporters.…”

Organization and Dynamics of the Red Blood Cell Band 3 Anion Exchanger SLC4A1: Insights From Molecular Dynamics Simulations

“…Band 3 residue R730 was shown to be critical for anion binding for both the entry and central binding sites. The cryo-electron microscopic structure of a sodium-dependent chloride/bicarbonate exchanger (SLC4A8) in the outward-facing state had well-defined densities for both the Na + close to D800 and bicarbonate in the central substrate binding site (Wang et al, 2021). Interestingly, the dimeric structure was further stabilized by a compact extracellular N-glycosylated domain between TM5 and 6 that contained two disulfide bonds.…”