[English] 日本語
Yorodumi
- PDB-9xro: LolCDE in complex with SMT-738_3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xro
TitleLolCDE in complex with SMT-738_3
Components
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Lipoprotein-releasing system transmembrane protein LolC
  • Lipoprotein-releasing system transmembrane protein LolE
KeywordsTRANSPORT PROTEIN / Bacterial lipoprotein transporter / LolCDE inhibitor / Cryo-EM / Allosteric conformational change
Function / homology
Function and homology information


lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain ...Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Lipoprotein-releasing system transmembrane protein LolC / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsDong, C.J. / Li, H.T.
Funding support China, 1items
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 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Lipoprotein-releasing system transmembrane protein LolC
E: Lipoprotein-releasing system transmembrane protein LolE
F: Lipoprotein-releasing system ATP-binding protein LolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6504
Polymers115,2583
Non-polymers3921
Water00
1


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

-
Components

#1: Protein Lipoprotein-releasing system transmembrane protein LolC


Mass: 43295.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0ADC3
#2: Protein Lipoprotein-releasing system transmembrane protein LolE


Mass: 45385.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolE, ycfW, b1118, JW1104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P75958
#3: Protein Lipoprotein-releasing system ATP-binding protein LolD


Mass: 26576.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolD, ycfV, b1117, JW5162 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#4: Chemical ChemComp-A1ER4 / 2-azanyl-1-[6-[2-azanyl-5-(3-methylpyridin-4-yl)-1H-imidazol-4-yl]-2,3-dihydro-1,4-benzoxazin-4-yl]-2-methyl-propan-1-one / SMT-738


Mass: 392.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N6O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: LolCDE in complex with SMT-738_3 / Type: COMPLEX / Details: an inhibitor SMT-738 bound LolCDE / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.115 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43(DE3)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
10.15 Msodium chlorideNaCl1
20.02 M2-Amino-2- (hydroxymethyl)-1,3-propanediolTris1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.1particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCv4.1CTF correction
13cryoSPARCv4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: OTHER / Num. of particles: 403023 / Symmetry type: POINT
RefinementHighest resolution: 2.88 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037353
ELECTRON MICROSCOPYf_angle_d0.6319985
ELECTRON MICROSCOPYf_dihedral_angle_d5.8741022
ELECTRON MICROSCOPYf_chiral_restr0.0451184
ELECTRON MICROSCOPYf_plane_restr0.0181273

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more