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- PDB-9w2w: Cryo-EM structure of two abaucin-bound LolDF in Acinetobacter bau... -

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Basic information

Entry
Database: PDB / ID: 9w2w
TitleCryo-EM structure of two abaucin-bound LolDF in Acinetobacter baumannii
Components
  • LolD
  • LolF
KeywordsMEMBRANE PROTEIN / Acinetobacter baumannii / LolFD / Nanodisc / Inhibitor
Function / homologyChem-R6Q
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, S. / Li, Y. / Liao, M.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFA0919900 China
National Natural Science Foundation of China (NSFC)32322004 China
National Natural Science Foundation of China (NSFC)32171205 China
National Natural Science Foundation of China (NSFC)U22A20338 China
Other government2023ZT10Y013
CitationJournal: Nat Commun / Year: 2026
Title: Structure and druggable conformation of the homodimeric lipoprotein transporter of Acinetobacter baumannii.
Authors: Song Zhang / Zhuyun Tang / Weiwei Shi / Jiaqi Su / Chao Che / Qi Xing / Maofu Liao / Yanyan Li /
Abstract: The growing crisis of antimicrobial resistance demands urgent need for antibiotics with alternative targets and modes of action (MOAs). Lipoproteins play crucial roles in bacterial survival and ...The growing crisis of antimicrobial resistance demands urgent need for antibiotics with alternative targets and modes of action (MOAs). Lipoproteins play crucial roles in bacterial survival and immunoregulation. The lipoprotein transporter, known as LolCDE or LolDF, has recently emerged as an effective target for selectively killing pathogenic bacteria such as Acinetobacter baumannii while sparing gut microbiota. While the heterodimeric LolCDE in Escherichia coli has been extensively studied, the druggable pocket and structural dynamics of the distinct homodimeric LolDF that exists in many critical pathogens are poorly understood. Such a knowledge gap limits our ability to exploit the Lol system to develop drugs with desired spectra of antibacterial activity. Here we determine the cryo-EM structures of homodimeric LolDF of A. baumannii in nucleotide-free apo-closed, vanadate-trapped fully closed, and inhibitor-bound open conformations, revealing the distinct structural features and conformational cycle of LolDF. Further cryo-EM, biochemical and functional analyses uncover the MOA of abaucin, a recently identified LolDF-targeting compound, demonstrating how multiple abaucin molecules open LolDF in a stepwise manner to establish an induced-fit pocket. Together, our results advance the understanding of LolDF function and inhibition, and provide the cryptic druggable conformation and specific inhibitor-bound pocket for structure-based drug discovery to target the dynamic lipoprotein transporter in A. baumannii.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LolF
D: LolD
B: LolF
C: LolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6536
Polymers137,8724
Non-polymers7812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein LolF


Mass: 44266.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC17978
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein LolD


Mass: 24669.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC17978
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-R6Q / 1'-[2-[4-(trifluoromethyl)phenyl]ethyl]spiro[1~{H}-3,1-benzoxazine-4,4'-piperidine]-2-one


Mass: 390.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 2ABA-bound AbLolFD / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: YES
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
12RELION3D reconstruction
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67055 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028232
ELECTRON MICROSCOPYf_angle_d0.39411286
ELECTRON MICROSCOPYf_dihedral_angle_d5.0581321
ELECTRON MICROSCOPYf_chiral_restr0.0391390
ELECTRON MICROSCOPYf_plane_restr0.0031475

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