7NDF | pdb_00007ndf

Crystal structure of nanobody Nb_MsbA#1 in complex with the nucleotide binding domain of MsbA

• PDB DOI: https://doi.org/10.2210/pdb7NDF/pdb

• Classification: PROTEIN BINDING
• Organism(s): Vicugna pacos, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-02-01 Released: 2022-03-02 
• Deposition Author(s): Meier, G., Seeger, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

• PubMed: 36223470 
• DOI: https://doi.org/10.1126/sciadv.abn6845
• Primary Citation 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.

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Organizational Affiliation: 
• Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany.
Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland.
Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland.
Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany.
Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany.
School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 78.93 kDa 
• Atom Count: 5,712 
• Modeled Residue Count: 707 
• Deposited Residue Count: 722 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb_MsbA 1	A [auth C], B [auth D]	116	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid A ABC transporter ATP-binding protein/permease MsbA	C [auth A], D [auth B]	245	Escherichia coli	Mutation(s): 0  Gene Names: msbA, HIR41_000141 EC: 7.5.2.6
UniProt
Find proteins for P60752 (Escherichia coli (strain K12)) Explore P60752  Go to UniProtKB:  P60752

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.53	α = 90
b = 99.3	β = 90
c = 142.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Meier, G., Seeger, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_188817

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary