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	The ABC transporter MsbA in a dozen environments.
Journal, issue, pages	Structure, Vol. 33, Issue 5, Page 916-923.e4, Year 2025
Publish date	May 1, 2025
Authors	Lea Hoffmann / Anika Baier / Lara Jorde / Michael Kamel / Jan-Hannes Schäfer / Kilian Schnelle / Alischa Scholz / Dmitry Shvarev / Jaslyn E M M Wong / Kristian Parey / Dovile Januliene / Arne Moeller /
PubMed Abstract	High-resolution structure determination of membrane proteins typically requires reconstitution into artificial membrane mimics. The choice of the specific membrane substitute can strongly affect the ...High-resolution structure determination of membrane proteins typically requires reconstitution into artificial membrane mimics. The choice of the specific membrane substitute can strongly affect the protein's specific activity, stability, and conformational spectrum, potentially leading to errors or misinterpretation during analysis. The bacterial ATP-binding cassette transporter MsbA is a prominent example of such environment-specific bias. Here, we present a systematic analysis of the conformational spectrum of MsbA, stabilized in a dozen environments, using cryoelectron microscopy (cryo-EM), and show pronounced feedback between the membrane mimetics and the transporter. Detergents generally favor wide inward-facing conformations while nanodiscs induce narrower conformations. Notably, only in three tested environments, MsbA samples the full movement of the nucleotide-binding domains, including narrow and wide conformations. We expect this study to serve as a blueprint for other membrane proteins, even where a structural reaction to the hydrophobic environment is not directly visible but still critical for the proteins' function.
External links	Structure / PubMed:40056915
Methods	EM (single particle)
Resolution	3.3 - 4.4 Å
Structure data	50774 9fuq EMDB-50774, PDB-9fuq: MsbA in DDM inward-facing wide open Method: EM (single particle) / Resolution: 3.8 Å 50775 9fur EMDB-50775, PDB-9fur: MsbA in LMNG inward-facing narrow Method: EM (single particle) / Resolution: 3.8 Å 50776 9fus EMDB-50776, PDB-9fus: MsbA in LMNG inward-facing wide open Method: EM (single particle) / Resolution: 3.8 Å 50777 9fut EMDB-50777, PDB-9fut: MsbA in GDN inward-facing narrow Method: EM (single particle) / Resolution: 3.8 Å 50778 9fuu EMDB-50778, PDB-9fuu: MsbA in GDN inward-facing wide open Method: EM (single particle) / Resolution: 3.6 Å 50779 9fuv EMDB-50779, PDB-9fuv: MsbA in Triton inward-facing wide open Method: EM (single particle) / Resolution: 4.0 Å 50780 9fuw EMDB-50780, PDB-9fuw: MsbA in Triton inward-facing wide (+) open Method: EM (single particle) / Resolution: 3.8 Å 50782 9fuy EMDB-50782, PDB-9fuy: MsbA in UDM inward-facing wide open Method: EM (single particle) / Resolution: 4.1 Å 50783 9fuz EMDB-50783, PDB-9fuz: MsbA in UDM inward-facing wide (+) open Method: EM (single particle) / Resolution: 4.2 Å 50784 9fv0 EMDB-50784, PDB-9fv0: MsbA in MSP1D1 Nanodisc inward-facing narrow open Method: EM (single particle) / Resolution: 3.9 Å 50785 9fv1 EMDB-50785, PDB-9fv1: MsbA in MSP1D1 (EPL:PC) Nanodisc inward-facing narrow open Method: EM (single particle) / Resolution: 3.8 Å 50786 9fv2 EMDB-50786, PDB-9fv2: MsbA in MSP1E3D1 Nanodisc inward-facing narrow open Method: EM (single particle) / Resolution: 3.3 Å 50787 9fv3 EMDB-50787, PDB-9fv3: MsbA in MSP2N2 Nanodisc inward-facing narrow open Method: EM (single particle) / Resolution: 3.9 Å 50788 9fv4 EMDB-50788, PDB-9fv4: MsbA in peptidisc inward-facing narrow (-) open Method: EM (single particle) / Resolution: 3.8 Å 50789 9fv5 EMDB-50789, PDB-9fv5: MsbA in peptidisc inward-facing narrow open Method: EM (single particle) / Resolution: 3.9 Å 50790 9fv6 EMDB-50790, PDB-9fv6: MsbA in Amphipol A8-35 inward-facing wide open Method: EM (single particle) / Resolution: 3.8 Å 50791 9fv7 EMDB-50791, PDB-9fv7: MsbA in Amphipol A8-35 inward-facing wide (+) open Method: EM (single particle) / Resolution: 4.0 Å 50792 9fv8 EMDB-50792, PDB-9fv8: MsbA in Amphipol 18 inward-facing wide open Method: EM (single particle) / Resolution: 3.4 Å 50793 9fv9 EMDB-50793, PDB-9fv9: MsbA in Amphipol 18 inward-facing wide (+) open Method: EM (single particle) / Resolution: 3.6 Å 50794 9fva EMDB-50794, PDB-9fva: MsbA in MSP2N2 Nanodisc inward-facing wide open Method: EM (single particle) / Resolution: 4.4 Å
Chemicals	ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM ChemComp-JSG: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid ChemComp-KDL*: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
Source	escherichia coli (E. coli)
Keywords	TRANSPORT PROTEIN / ABC transporter