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- PDB-9j3e: Cryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthyl... -

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Basic information

Entry
Database: PDB / ID: 9j3e
TitleCryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthylmethyl)piperazine
Components
  • Efflux pump membrane transporter
  • RND efflux system, MexC-like protein
  • RND efflux system, OprJ-like protein
KeywordsTRANSPORT PROTEIN / efflux pump / transporter / antibiotics / antimicrobial resistance
Function / homology
Function and homology information


efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / response to toxic substance / response to antibiotic / plasma membrane
Similarity search - Function
RND efflux system, outer membrane lipoprotein, NodT / : / : / RND MFP, alpha-helical hairpin domain / RND MFPs, beta-barrel domain / : / RND MFPs, C-terminal permuted SH3 domain / : / RND MFP, barrel-sandwich hybrid domain / RND efflux pump, membrane fusion protein ...RND efflux system, outer membrane lipoprotein, NodT / : / : / RND MFP, alpha-helical hairpin domain / RND MFPs, beta-barrel domain / : / RND MFPs, C-terminal permuted SH3 domain / : / RND MFP, barrel-sandwich hybrid domain / RND efflux pump, membrane fusion protein / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / RND efflux system, MexC-like protein / Efflux pump membrane transporter / RND efflux system, OprJ-like protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsShi, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Assembly and inhibition of transferable TMexCD1-TOprJ1 efflux pump.
Authors: Yu Shi / Mengyuan Li / Tao Cui / Jianhua Gan / Haomin Huang / Zhi Su / Runshi Yang / Xing Zhang / Huimin Zhang / Yu Feng / Youjun Feng /
Abstract: Recent emergence and dissemination of plasmid-borne tmexCD1-toprJ1 tigecycline resistance threatens the efficacy of tigecycline as a "last-resort" defense against bacterial infections. Here, we ...Recent emergence and dissemination of plasmid-borne tmexCD1-toprJ1 tigecycline resistance threatens the efficacy of tigecycline as a "last-resort" defense against bacterial infections. Here, we report two cryo-EM structures of TMexCD1-TOprJ1 alone and in complex with its NMP inhibitor, and both are determined at the resolutions of 2.97 Å and 3.0 Å, respectively. The symmetry of overall architecture explains how the tripartite organization adopts a 3:6:3 protomer stoichiometry (TOprJ1: TMexC1: TMexD1) to assemble an elongated, rod-like pump spanning bacterial double membranes. The periplasmic TMexC1 adaptor bind the trimeric TOprJ1 funnel via a universal "tip-to-tip" contact, and bridges the bottom TMexD1 engine by extensive interactions. A unique form of resting (R) states is observed for TMexD1 trimer. Besides two binding-interfaces of TMexC1 with TOprJ1 and TMexD1, we characterize a substrate/inhibitor-loading cavity. Collectively, these findings constitute molecular bases for assembly and inhibition of transferable TMexCD1-TOprJ1 machinery, and benefit developing next-generation of antimicrobials targeting functional efflux pump.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RND efflux system, OprJ-like protein
B: RND efflux system, OprJ-like protein
C: RND efflux system, OprJ-like protein
D: RND efflux system, MexC-like protein
E: RND efflux system, MexC-like protein
F: RND efflux system, MexC-like protein
G: RND efflux system, MexC-like protein
H: RND efflux system, MexC-like protein
I: RND efflux system, MexC-like protein
K: Efflux pump membrane transporter
J: Efflux pump membrane transporter
L: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)750,80915
Polymers750,13012
Non-polymers6793
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 RND efflux system, OprJ-like protein


Mass: 52397.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411AKN6
#2: Protein
RND efflux system, MexC-like protein


Mass: 42678.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411AKL2
#3: Protein Efflux pump membrane transporter


Mass: 112289.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411AKL6
#4: Chemical ChemComp-A1EAN / 1-(naphthalen-1-ylmethyl)piperazine / 40675-81-8


Mass: 226.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H18N2 / 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: TMexCD1-TOprJ1 / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: FEI TITAN 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: 51.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52844 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00648669
ELECTRON MICROSCOPYf_angle_d0.8366108
ELECTRON MICROSCOPYf_dihedral_angle_d4.4986927
ELECTRON MICROSCOPYf_chiral_restr0.0467755
ELECTRON MICROSCOPYf_plane_restr0.0068724

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