8ZI2 | pdb_00008zi2

Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM reveals transition states of the Acinetobacter baumannii F 1 -ATPase rotary subunits gamma and epsilon , unveiling novel compound targets.

Le, K.C.M.Wong, C.F.Muller, V.Gruber, G.

(2024) FASEB J 38: e70131-e70131

  • DOI: https://doi.org/10.1096/fj.202401629R
  • Primary Citation of Related Structures:  
    8ZI0, 8ZI1, 8ZI2, 8ZI3

  • PubMed Abstract: 

    Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional F 1 F O -ATP synthase. While synthesizing ATP, it regulates ATP cleavage by its inhibitory ε subunit to prevent wasteful ATP consumption. We determined cryo-electron microscopy structures of the ATPase active A. baumannii F 1 -αßγε Δ134-139 mutant in four distinct conformational states, revealing four transition states and structural transformation of the ε's C-terminal domain, forming the switch of an ATP hydrolysis off- and an ATP synthesis on-state based. These alterations go in concert with altered motions and interactions in the catalytic- and rotary subunits of this engine. These A. baumannii interacting sites provide novel pathogen-specific targets for inhibitors, with the aim of ATP depletion and/or ATP synthesis and growth inhibition. Furthermore, the presented diversity to other bacterial F-ATP synthases extends the view of structural elements regulating such a catalyst.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
514Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: atpAA1S_0153
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A3M142 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M142 
Go to UniProtKB:  A3M142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M142
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
464Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A3M144 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M144 
Go to UniProtKB:  A3M144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M144
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainG [auth e]133Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for A3M145 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M145 
Go to UniProtKB:  A3M145
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M145
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chainH [auth g]289Acinetobacter baumannii AB5075Mutation(s): 0 
Gene Names: atpGA1S_0154
Membrane Entity: Yes 
UniProt
Find proteins for A3M143 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377))
Explore A3M143 
Go to UniProtKB:  A3M143
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3M143
Sequence Annotations
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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 A],
K [auth B],
N [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
O [auth D]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 A],
L [auth B],
M [auth C],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeRG20/22

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release