7FC9

Crystal structure of CmABCB1 in lipidic mesophase revealed by LCP-SFX

Summary for 7FC9

• Entry DOI: 10.2210/pdb7fc9/pdb
• Descriptor: Probable ATP-dependent transporter ycf16, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ZINC ION, ... (7 entities in total)
• Functional Keywords: multi-drug exporter, transport protein
• Biological source: Cyanidioschyzon merolae (strain 10D) (Red alga)
• Total number of polymer chains: 1
• Total formula weight: 65449.06

Authors

Pan, D.,Oyama, R.,Sato, T.,Nakane, T.,Mizunuma, R.,Matsuoka, K.,Joti, Y.,Tono, K.,Nango, E.,Iwata, S.,Nakatsu, T.,Kato, H. (deposition date: 2021-07-14, release date: 2022-02-02, Last modification date: 2023-11-29)

Primary citation

Pan, D.,Oyama, R.,Sato, T.,Nakane, T.,Mizunuma, R.,Matsuoka, K.,Joti, Y.,Tono, K.,Nango, E.,Iwata, S.,Nakatsu, T.,Kato, H.
Crystal structure of CmABCB1 multi-drug exporter in lipidic mesophase revealed by LCP-SFX.
Iucrj, 9:134-145, 2022

PubMed Abstract: CmABCB1 is a homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open-close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono-acyl-glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy-droxy-propyl methyl-cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.

PubMed: 35059217
DOI: 10.1107/S2052252521011611

Experimental method

X-RAY DIFFRACTION (2.2 Å)