9BD6 | pdb_00009bd6

PaMsbA in an occluded, outward conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9BD6

This is version 1.1 of the entry. See complete history

Literature

Molecular Basis for the Activation of Pseudomonas aeruginosa MsbA by Divalent Metals.

Lyu, J.Bahramimoghaddam, H.Zhang, T.Scott, E.Yun, S.D.Yadav, G.P.Zhao, M.Russell, D.Laganowsky, A.

(2025) J Am Chem Soc 147: 31488-31496

  • DOI: https://doi.org/10.1021/jacs.4c18759
  • Primary Citation Related Structures: 
    9BD6, 9BD7

  • PubMed Abstract: 

    Proteins involved in the biogenesis of lipopolysaccharide (LPS), a lipid exclusive to Gram-negative bacteria, are promising candidates for drug discovery. Specifically, the ABC transporter MsbA plays a crucial role in translocating an LPS precursor from the cytoplasmic to the periplasmic facing leaflet of the inner membrane, and small molecules that inhibit its function exhibit bactericidal activity. Here, we use native mass spectrometry (MS) to determine lipid binding affinities of MsbA from P. aeruginosa (PaMsbA), a Gram-negative bacteria associated with hospital-acquired infections, in different conformations. Unlike the transporter from E. coli , we show that the ATPase activity of PaMsbA is stimulated by Zn 2+ , Ni 2+ , and Mn 2+ and successfully trapping the protein with vanadate requires one of these metal ions. We also present cryogenic-electron microscopy structures of PaMsbA in occluded and open outward-facing conformations determined to resolutions of 2.58 and 2.44 Å, respectively. The structures reveal a triad of histidine residues, and mutation of these residues abolishes Zn 2+ binding and stimulation of PaMsbA activity by metal ions. Together, our studies provide insight into the structure of PaMsbA and its lipid binding preferences and reveal that a subset of divalent metals stimulates its ATPase activity.


  • Organizational Affiliation
    • Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.

Macromolecule Content 

  • Total Structure Weight: 134.74 kDa 
  • Atom Count: 9,028 
  • Modeled Residue Count: 1,152 
  • Deposited Residue Count: 1,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent lipid A-core flippase
A, B
605Pseudomonas aeruginosaMutation(s): 0 
Gene Names: msbAPA4997
EC: 7.5.2.6
Membrane Entity: Yes 
UniProt
Find proteins for Q9HUG8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HUG8 
Go to UniProtKB:  Q9HUG8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HUG8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AD9
(Subject of Investigation/LOI)

Query on AD9



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
ADP METAVANADATE
C10 H16 N5 O13 P2 V
XLVFTLJPBLXCED-KWIZKVQNSA-K
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]
E [auth A]
F [auth A]
G [auth B]
I [auth B]
C [auth A],
E [auth A],
F [auth A],
G [auth B],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM138863
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM139876
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM1454316

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Data collection, Database references