Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 2653, Year 2025
Publish date	Mar 20, 2025
Authors	Daisuke Kozai / Masao Inoue / Shota Suzuki / Akiko Kamegawa / Kouki Nishikawa / Hiroshi Suzuki / Toru Ekimoto / Mitsunori Ikeguchi / Yoshinori Fujiyoshi /
PubMed Abstract	Aquaglyceroporins such as aquaporin-3 (AQP3) and its bacterial homologue GlpF facilitate water and glycerol permeation across lipid bilayers. X-ray crystal structures of GlpF showed open pore ...Aquaglyceroporins such as aquaporin-3 (AQP3) and its bacterial homologue GlpF facilitate water and glycerol permeation across lipid bilayers. X-ray crystal structures of GlpF showed open pore conformations, and AQP3 has also been predicted to adopt this conformation. Here we present cryo-electron microscopy structures of rat AQP3 and GlpF in different narrowed pore conformations. In n-dodecyl-β-D-maltopyranoside detergent micelles, aromatic/arginine constriction filter residues of AQP3 containing Tyr212 form a 2.8-Å diameter pore, whereas in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) nanodiscs, Tyr212 inserts into the pore. Molecular dynamics simulation shows the Tyr212-in conformation is stable and largely suppresses water permeability. AQP3 reconstituted in POPC liposomes exhibits water and glycerol permeability, suggesting that the Tyr212-in conformation may be altered during permeation. AQP3 Y212F and Y212T mutant structures suggest that the aromatic residue drives the pore-inserted conformation. The aromatic residue is conserved in AQP7 and GlpF, but neither structure exhibits the AQP3-like conformation in POPC nanodiscs. Unexpectedly, the GlpF pore is covered by an intracellular loop, but the loop is flexible and not primarily related to the GlpF permeability. Our findings illuminate the unique AQP3 conformation and structural diversity of aquaglyceroporins.
External links	Nat Commun / PubMed:40113770 / PubMed Central
Methods	EM (single particle)
Resolution	2.26 - 3.74 Å
Structure data	39052 8y8n EMDB-39052, PDB-8y8n: Cryo-EM structure of AQP3 in DDM micelle Method: EM (single particle) / Resolution: 3.12 Å 39053 8y8o EMDB-39053, PDB-8y8o: Cryo-EM structure of AQP3 in POPC nanodisc Method: EM (single particle) / Resolution: 2.94 Å 39054 8y8p EMDB-39054, PDB-8y8p: Cryo-EM structure of AQP3 Y212F in POPC nanodisc Method: EM (single particle) / Resolution: 2.9 Å 39055 8y8q EMDB-39055, PDB-8y8q: Cryo-EM structure of AQP3 Y212T in POPC nanodisc Method: EM (single particle) / Resolution: 2.67 Å 39056 8y8r EMDB-39056, PDB-8y8r: Cryo-EM structure of AQP3 Y212T in DDM micelle Method: EM (single particle) / Resolution: 3.39 Å 39057 8y8s EMDB-39057, PDB-8y8s: Cryo-EM structure of AQP3 in DMPC nanodisc Method: EM (single particle) / Resolution: 3.03 Å 39060 8y8v EMDB-39060, PDB-8y8v: Cryo-EM structure of AQP7 in POPC nanodisc Method: EM (single particle) / Resolution: 2.49 Å EMDB-39061: Cryo-EM map of GlpF in DDM micelle Method: EM (single particle) / Resolution: 3.74 Å 39062 8y8w EMDB-39062, PDB-8y8w: Cryo-EM structure of GlpF in POPC nanodisc Method: EM (single particle) / Resolution: 2.43 Å 39063 8y8x EMDB-39063, PDB-8y8x: Cryo-EM structure of GlpF with P177 deletion in POPC nanodisc Method: EM (single particle) / Resolution: 2.26 Å
Chemicals	ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-P5S*: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
Source	rattus norvegicus (Norway rat) homo sapiens (human) escherichia coli (E. coli) aequorea victoria (jellyfish)
Keywords	MEMBRANE PROTEIN / water channel / aquaporin / aquaglyceroporin / glycerol