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- EMDB-65592: Cryo-EM structure of nucleotide-free LolDF in Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-65592
TitleCryo-EM structure of nucleotide-free LolDF in Acinetobacter baumannii
Map data
Sample
  • Complex: Nucleotide-free AbLolFD
    • Protein or peptide: LolD
    • Protein or peptide: LolF
KeywordsAcinetobacter baumannii / LolFD / Nanodisc / nucleotide-free / MEMBRANE PROTEIN
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZhang S / Li Y / Liao M
Funding support China, 5 items
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 29, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65592.png

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Map

FileReleased
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.049382053 - 0.0651388
Average (Standard dev.)0.000034943016 (±0.00238262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65592_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_65592_half_map_2.map
Projections & Slices
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Sample components

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Entire : Nucleotide-free AbLolFD

EntireName: Nucleotide-free AbLolFD
Components
  • Complex: Nucleotide-free AbLolFD
    • Protein or peptide: LolD
    • Protein or peptide: LolF

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Supramolecule #1: Nucleotide-free AbLolFD

SupramoleculeName: Nucleotide-free AbLolFD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: LolD

MacromoleculeName: LolD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: ATCC17978
Molecular weightTheoretical: 24.669271 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: KVVLEAKDIY KHFDDGKSKV EVIKGLSLQV EAGQFVSIVG ASGSGKSTLL HVLGGLDQPT KGQVFLNGQR FDNLGEAERG FQRNQYLGF VYQFHHLLPE FTALENVAMP LMLRADSQYK SVKAQAEYLL DRVGLSHRMD HKPGELSGGE RQRVALARAL V TKPAVVLA ...String:
KVVLEAKDIY KHFDDGKSKV EVIKGLSLQV EAGQFVSIVG ASGSGKSTLL HVLGGLDQPT KGQVFLNGQR FDNLGEAERG FQRNQYLGF VYQFHHLLPE FTALENVAMP LMLRADSQYK SVKAQAEYLL DRVGLSHRMD HKPGELSGGE RQRVALARAL V TKPAVVLA DEPTGNLDRK TAVGIFELLT DLKKELQMAM LIVTHDEQLA QAADSILHME DGLWV

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Macromolecule #2: LolF

MacromoleculeName: LolF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: ATCC17978
Molecular weightTheoretical: 44.266871 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MFKPISLYIG LRYTRARRSN HFISFIALVS MVGLTLGVAV LITVLSVMNG FDRELKNRVL GMVPQATVSS TQILTDWPEL VKRVENHPH VTGVAPFTQL QGMLTAQGQV AGIMVTGIDP KYEKNVSIIQ NHIVAGSLDS LKKGEFGIVL GKDMADSLGL R LNDSVTLV ...String:
MFKPISLYIG LRYTRARRSN HFISFIALVS MVGLTLGVAV LITVLSVMNG FDRELKNRVL GMVPQATVSS TQILTDWPEL VKRVENHPH VTGVAPFTQL QGMLTAQGQV AGIMVTGIDP KYEKNVSIIQ NHIVAGSLDS LKKGEFGIVL GKDMADSLGL R LNDSVTLV LPEATPSPAG VVPRFKRFKV VGIFSVGAEV DSMVGYIALY DASTLLRLPD GAQGVRLKLD DIFAAPQVAD DI VKNLPSN FYATNWTYTH GNLFNAIQME KTLVGLLLVL IIVVAAFNIV SSLVMVVTDK KSDIAILRTL GASPSMITKI FMV QGTVIG VIGTVAGTVL GVILALTISD IISWFNNVLG LNLFDAYFVH YLPSYLRWQD VTIIVIVSLL LSFLATIYPA LRAA KVQPA EAL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45074
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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