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 24DM | pdb_000024dm

Structural snapshots of F1-ATPase catalysis in drug resistant Acinetobacter baumannii reveal novel therapeutic targets - Conformation 3a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 24DM

This is version 1.0 of the entry. See complete history. 

Literature

Structural Snapshots of F 1 -ATPase Catalysis in Drug Resistant Acinetobacter baumannii Reveal Novel Therapeutic Targets.

Le, K.C.M., Marzinek, J.K., Mathiyazakan, V., Bond, P.J., Gruber, G.

(2026) FASEB J 40: e72385-e72385

  • DOI: https://doi.org/10.1096/fj.202602735R
  • Primary Citation Related Structures: 
    24DH, 24DJ, 24DK, 24DL, 24DM, 24DN

  • PubMed Abstract: 

    Gram-negative Acinetobacter baumannii, one of the most critical priority pathogens, has developed multiple defense mechanisms, including upregulation of drug efflux pumps powered by the proton-motive force (pmf) or ATP. As a nonfermenting bacterium, it relies on oxidative phosphorylation, in which the F-ATP synthase, composed of an F 1 -ATPase (α 3 :β 3 :γ:ε) and F O -domain (a:b 2 :c 10 ), synthesizes ATP, the cell's currency of life. Here, we present cryo-electron microscopy structures of the F 1 -ATPase captured during ATP synthesis, revealing concerted conformational changes within the α 3 :β 3 -catalytic head that trigger structural transitions of subunit ε and twisting of the γ:ε central stalk, coupled with spontaneous ATP formation. Molecular dynamics simulations validate and expand the ensemble of structural rearrangements underlying the rotary mechanism. The resolved intermediate states of the ε subunit reveal its role as a molecular gear, regulating ATP synthesis while simultaneously inhibiting ATP hydrolysis, essential for the pathogen to prevent wastage of ATP. These structural snapshots identify novel therapeutic targets and pave the way for rational design of selective inhibitors.


  • Organizational Affiliation: 
    • School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore.

Macromolecule Content 

  • Total Structure Weight: 367.03 kDa 
  • Atom Count: 24,625 
  • Modeled Residue Count: 3,249 
  • Deposited Residue Count: 3,362 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainA [auth e]139Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VHG0 (Acinetobacter baumannii)
Explore V5VHG0 
Go to UniProtKB:  V5VHG0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VHG0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaB,
C,
H [auth A]
514Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
EC: 7.1.2.2
UniProt
Find proteins for V5VJ37 (Acinetobacter baumannii)
Explore V5VJ37 
Go to UniProtKB:  V5VJ37
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VJ37
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit betaD,
E [auth F],
G [auth E]
464Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
EC: 7.1.2.2
UniProt
Find proteins for V5VHQ6 (Acinetobacter baumannii)
Explore V5VHQ6 
Go to UniProtKB:  V5VHQ6
Entity Groups
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UniProt GroupV5VHQ6
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chainF [auth g]289Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for V5VHZ7 (Acinetobacter baumannii)
Explore V5VHZ7 
Go to UniProtKB:  V5VHZ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5VHZ7
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
I [auth B],
L [auth C],
Q [auth E],
R [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
N [auth D],
O [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
J [auth B],
K [auth C],
M [auth C],
P [auth E],
S [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF- CRP27-2021-0002

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release