8GK7

MsbA bound to cerastecin C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cerastecins inhibit membrane lipooligosaccharide transport in drug-resistant Acinetobacter baumannii.

Wang, H.Ishchenko, A.Skudlarek, J.Shen, P.Dzhekieva, L.Painter, R.E.Chen, Y.T.Bukhtiyarova, M.Leithead, A.Tracy, R.Babaoglu, K.Bahnck-Teets, C.Buevich, A.Cabalu, T.D.Labroli, M.Lange, H.Lei, Y.Li, W.Liu, J.Mann, P.A.Meng, T.Mitchell, H.J.Mulhearn, J.Scapin, G.Sha, D.Shaw, A.W.Si, Q.Tong, L.Wu, C.Wu, Z.Xiao, J.C.Xu, M.Zhang, L.K.McKenney, D.Miller, R.R.Black, T.A.Cooke, A.Balibar, C.J.Klein, D.J.Raheem, I.Walker, S.S.

(2024) Nat Microbiol 

  • DOI: https://doi.org/10.1038/s41564-024-01667-0
  • Primary Citation of Related Structures:  
    8GK7

  • PubMed Abstract: 

    Carbapenem-resistant Acinetobacter baumannii infections have limited treatment options. Synthesis, transport and placement of lipopolysaccharide or lipooligosaccharide (LOS) in the outer membrane of Gram-negative bacteria are important for bacterial virulence and survival. Here we describe the cerastecins, inhibitors of the A. baumannii transporter MsbA, an LOS flippase. These molecules are potent and bactericidal against A. baumannii, including clinical carbapenem-resistant Acinetobacter baumannii isolates. Using cryo-electron microscopy and biochemical analysis, we show that the cerastecins adopt a serpentine configuration in the central vault of the MsbA dimer, stalling the enzyme and uncoupling ATP hydrolysis from substrate flipping. A derivative with optimized potency and pharmacokinetic properties showed efficacy in murine models of bloodstream or pulmonary A. baumannii infection. While resistance development is inevitable, targeting a clinically unexploited mechanism avoids existing antibiotic resistance mechanisms. Although clinical validation of LOS transport remains undetermined, the cerastecins may open a path to narrow-spectrum treatment modalities for important nosocomial infections.


  • Organizational Affiliation

    Merck & Co., Inc., West Point, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipid A export ATP-binding/permease protein MsbA
A, B
598Acinetobacter baumanniiMutation(s): 0 
Gene Names: msbA
Membrane Entity: Yes 
UniProt
Find proteins for A0A6F8TGG1 (Acinetobacter baumannii)
Explore A0A6F8TGG1 
Go to UniProtKB:  A0A6F8TGG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6F8TGG1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZQF (Subject of Investigation/LOI)
Query on ZQF

Download Ideal Coordinates CCD File 
D [auth A]2-[(4-butylbenzene-1-sulfonyl)amino]-5-[(3-{4-[(4-butylbenzene-1-sulfonyl)amino]-3-carboxyanilino}-3-oxopropyl)carbamoyl]benzoic acid
C38 H42 N4 O10 S2
SXEMELNAPRMMRT-UHFFFAOYSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references