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- EMDB-67112: LolCDE in complex with SMT-738_1 -

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Basic information

Entry
Database: EMDB / ID: EMD-67112
TitleLolCDE in complex with SMT-738_1
Map dataLolCDE-SMT-738_map_sharp
Sample
  • Complex: LolCDE in complex with SMT-738_1
KeywordsBacterial lipoprotein transporter / LolCDE inhibitor / Cryo-EM / Allosteric conformational change / TRANSPORT PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsDong CJ / Li HT
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303500 China
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanism of action of small molecule SMT-738 on bacterial lipoprotein transporter LolCDE.
Authors: Haotian Li / Xiaojing Zhu / Dongdong Zhang / Xiaofeng Duan / Jiahui Li / Yao Qu / Danyang Li / Zhengyu Zhang / Haohao Dong / Feng-Biao Guo / Changjiang Dong /
Abstract: SMT-738 is a small molecule with promising antibacterial activity against Enterobacteriaceae, including multi-drug-resistant Escherichia coli. Mutations in genes encoding the lipoprotein transport ...SMT-738 is a small molecule with promising antibacterial activity against Enterobacteriaceae, including multi-drug-resistant Escherichia coli. Mutations in genes encoding the lipoprotein transport complex (LolCDE) confer resistance to SMT-738. Here, we report the cryogenic electron microscopy structure of the LolCDE-SMT-738 complex at a high resolution. We use mutagenesis, drug resistance assays, biochemical assays, and molecular dynamics simulations to show that SMT-738 binds to the periplasmic end of the LolCE transmembrane domains. This binding induces an allosteric conformational change in the cytoplasmic end of the LolCE transmembrane domains and the coupling helices, leading to dissociation of one LolD subunit from the LolCDE complex. This structural disruption results in a "deadlock" of the LolCDE complex, rendering a transport-incompetent state. Our findings also provide insights into the mechanism of SMT-738 resistance and selectivity.
History
DepositionNov 18, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67112.png

Downloads & links

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Map

FileDownload / File: emd_67112.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLolCDE-SMT-738_map_sharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-1.3652399 - 1.8391479
Average (Standard dev.)-0.00018244187 (±0.029524628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: LolCDE-SMT-738 map half B

Fileemd_67112_half_map_1.map
AnnotationLolCDE-SMT-738_map_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LolCDE-SMT-738 map half A

Fileemd_67112_half_map_2.map
AnnotationLolCDE-SMT-738_map_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LolCDE in complex with SMT-738_1

EntireName: LolCDE in complex with SMT-738_1
Components
  • Complex: LolCDE in complex with SMT-738_1

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Supramolecule #1: LolCDE in complex with SMT-738_1

SupramoleculeName: LolCDE in complex with SMT-738_1 / type: complex / ID: 1 / Parent: 0 / Details: an inhibitor SMT-738 bound LolCDE
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 115 KDa

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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

Concentration1.0 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
0.15 MNaClsodium chloride
0.02 MTris2-Amino-2- (hydroxymethyl)-1,3-propanediol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

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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: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1) / Number images used: 403023
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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