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Structure paper

TitleThe ABC transporter MsbA adopts the wide inward-open conformation in cells.
Journal, issue, pagesSci Adv, Vol. 8, Issue 41, Page eabn6845, Year 2022
Publish dateOct 14, 2022
AuthorsLaura Galazzo / Gianmarco Meier / Dovile Januliene / Kristian Parey / Dario De Vecchis / Bianca Striednig / Hubert Hilbi / Lars V Schäfer / Ilya Kuprov / Arne Moeller / Enrica Bordignon / Markus A Seeger /
PubMed AbstractMembrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their ...Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
External linksSci Adv / PubMed:36223470 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.1 - 4.1 Å
Structure data

13404

7ph2

EMDB-13404, PDB-7ph2:
Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position A60C
Method: EM (single particle) / Resolution: 3.7 Å

13405

7ph3

EMDB-13405, PDB-7ph3:
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C
Method: EM (single particle) / Resolution: 2.8 Å

13406

7ph4

EMDB-13406, PDB-7ph4:
AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position T68C
Method: EM (single particle) / Resolution: 2.8 Å

13409

7ph7

EMDB-13409, PDB-7ph7:
Nanodisc reconstituted MsbA in complex with nanobodies, spin-labeled at position T68C
Method: EM (single particle) / Resolution: 4.1 Å

PDB-7ndf:
Crystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of MsbA
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-EIW:
(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{S},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},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-3,5-bis(oxidanyl)oxan-2-yl]oxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{R})-3-nonanoyloxytetradecanoyl]oxy-5-[[(3~{R})-3-octanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanylnonanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-oxan-2-yl]methoxy]-5-oxidanyl-oxane-2-carboxylic acid

ChemComp-88T:
(1~{R},4~{R},11~{S},14~{S},19~{Z})-19-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylimino]-7,8,17,18-tetraoxa-1,4,11,14-tetrazatricyclo[12.6.2.2^{4,11}]tetracosane-6,9,16-trione

ChemComp-GD:
GADOLINIUM ATOM

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

Source
  • escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
  • vicugna pacos (alpaca)
  • escherichia coli (strain k12) (bacteria)
KeywordsPROTEIN BINDING / nucleotide binding domain / ABC transporter / nanobody / MEMBRANE PROTEIN / Gd-DOTA / AMP-PNP / lipid A

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