9FV7 | pdb_00009fv7

MsbA in Amphipol A8-35 inward-facing wide (+) open


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9FV7

This is version 1.2 of the entry. See complete history

Literature

The ABC transporter MsbA in a dozen environments.

Hoffmann, L.Baier, A.Jorde, L.Kamel, M.Schafer, J.H.Schnelle, K.Scholz, A.Shvarev, D.Wong, J.E.M.M.Parey, K.Januliene, D.Moeller, A.

(2025) Structure 33: 916

  • DOI: https://doi.org/10.1016/j.str.2025.02.002
  • Primary Citation Related Structures: 
    9FUQ, 9FUR, 9FUS, 9FUT, 9FUU, 9FUV, 9FUW, 9FUY, 9FUZ, 9FV0, 9FV1, 9FV2, 9FV3, 9FV4, 9FV5, 9FV6, 9FV7, 9FV8, 9FV9, 9FVA

  • 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 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.


  • Organizational Affiliation
    • Osnabrück University, Department of Biology/Chemistry, Structural Biology Section, 49076 Osnabrück, Germany.

Macromolecule Content 

  • Total Structure Weight: 129.06 kDa 
  • Atom Count: 8,822 
  • Modeled Residue Count: 1,138 
  • Deposited Residue Count: 1,164 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent lipid A-core flippaseA [auth B],
B [auth A]
582Escherichia coliMutation(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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 944
German Research Foundation (DFG)GermanySFB 1557
German Research Foundation (DFG)GermanyINST190/196-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection