7PH3

AMP-PNP bound nanodisc reconstituted MsbA with nanobodies, spin-labeled at position A60C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells.

Galazzo, L.Meier, G.Januliene, D.Parey, K.De Vecchis, D.Striednig, B.Hilbi, H.Schafer, L.V.Kuprov, I.Moeller, A.Bordignon, E.Seeger, M.A.

(2022) Sci Adv 8: eabn6845-eabn6845

  • DOI: https://doi.org/10.1126/sciadv.abn6845
  • Primary Citation of Related Structures:  
    7NDF, 7PH2, 7PH3, 7PH4, 7PH7

  • PubMed Abstract: 

    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 Escherichia coli 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.


  • Organizational Affiliation

    Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent lipid A-core flippase
A, B
593Escherichia coli K-12Mutation(s): 0 
Gene Names: msbAb0914JW0897
EC: 7.5.2.6
Membrane Entity: Yes 
UniProt
Find proteins for P60752 (Escherichia coli (strain K12))
Explore P60752 
Go to UniProtKB:  P60752
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60752
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody Nb_MsbA#1
C, D
117Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
88T (Subject of Investigation/LOI)
Query on 88T

Download Ideal Coordinates CCD File 
M [auth C],
O [auth D]
(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
C22 H32 N6 O9
KCVYYVOXIBCERI-QJOMJCCJSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GD (Subject of Investigation/LOI)
Query on GD

Download Ideal Coordinates CCD File 
N [auth C],
P [auth D]
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.0.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyCRC944
German Research Foundation (DFG)GermanySCHA 1574/6-1
German Research Foundation (DFG)GermanyEXC 2033 - 390677874 - RESOLV

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary