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	Structural basis of closed groove scrambling by a TMEM16 protein.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 10, Page 1468-1481, Year 2024
Publish date	Apr 29, 2024
Authors	Zhang Feng / Omar E Alvarenga / Alessio Accardi /
PubMed Abstract	Activation of Ca-dependent TMEM16 scramblases induces phosphatidylserine externalization, a key step in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by ...Activation of Ca-dependent TMEM16 scramblases induces phosphatidylserine externalization, a key step in multiple signaling processes. Current models suggest that the TMEM16s scramble lipids by deforming the membrane near a hydrophilic groove and that Ca dependence arises from the different association of lipids with an open or closed groove. However, the molecular rearrangements underlying groove opening and how lipids reorganize outside the closed groove remain unknown. Here we directly visualize how lipids associate at the closed groove of Ca-bound fungal nhTMEM16 in nanodiscs using cryo-EM. Functional experiments pinpoint lipid-protein interaction sites critical for closed groove scrambling. Structural and functional analyses suggest groove opening entails the sequential appearance of two π-helical turns in the groove-lining TM6 helix and identify critical rearrangements. Finally, we show that the choice of scaffold protein and lipids affects the conformations of nhTMEM16 and their distribution, highlighting a key role of these factors in cryo-EM structure determination.
External links	Nat Struct Mol Biol / PubMed:38684930
Methods	EM (single particle)
Resolution	2.64 - 4.07 Å
Structure data	41453 8toi EMDB-41453, PDB-8toi: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state) Method: EM (single particle) / Resolution: 2.64 Å 41454 8tok EMDB-41454, PDB-8tok: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (open state) Method: EM (single particle) / Resolution: 3.84 Å 41455 8tol EMDB-41455, PDB-8tol: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (open state) Method: EM (single particle) / Resolution: 2.85 Å EMDB-41457: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state) (consensus map) Method: EM (single particle) / Resolution: 2.64 Å EMDB-41458: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (closed state)(local refined monomer map) Method: EM (single particle) / Resolution: 2.64 Å 41477 8tpm EMDB-41477, PDB-8tpm: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP1E3 scaffold protein in the absence of Ca2+ Method: EM (single particle) / Resolution: 2.93 Å 41478 8tpn EMDB-41478, PDB-8tpn: nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (intermediate state) Method: EM (single particle) / Resolution: 4.07 Å 41479 8tpo EMDB-41479, PDB-8tpo: nhTMEM16 R432A mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ Method: EM (single particle) / Resolution: 3.59 Å 41480 8tpp EMDB-41480, PDB-8tpp: nhTMEM16 R432A mutant in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ Method: EM (single particle) / Resolution: 3.64 Å 41481 8tpq EMDB-41481, PDB-8tpq: nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6) Method: EM (single particle) / Resolution: 3.35 Å 41482 8tpr EMDB-41482, PDB-8tpr: nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (short TM6) Method: EM (single particle) / Resolution: 2.85 Å 41483 8tps EMDB-41483, PDB-8tps: nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (bent TM6) Method: EM (single particle) / Resolution: 2.97 Å 41484 8tpt EMDB-41484, PDB-8tpt: nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6/short TM6) Method: EM (single particle) / Resolution: 3.01 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl / phospholipid*YM
Source	fusarium vanettenii 77-13-4 (fungus) fusarium vanettenii (fungus)
Keywords	LIPID TRANSPORT / membrane protein / lipid scramblase / TMEM16