[English] 日本語
Yorodumi
- PDB-9lyj: Cryo-EM structure of MdtF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lyj
TitleCryo-EM structure of MdtF
ComponentsMultidrug resistance protein MdtF
KeywordsTRANSPORT PROTEIN / Membrane protein / E.coli. / Cryo-EM / Efflux pump.
Function / homology
Function and homology information


xenobiotic transmembrane transport / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / response to toxic substance / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Multidrug resistance protein MdtF
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsDutta, S. / Padmanaban, S. / Fernando, R.C.
Funding support India, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Science and Engineering Research Board (SERB)CRG/2022/002674 India
CitationJournal: mBio / Year: 2026
Title: Cryo-EM reveals the structural heterogeneity and conformational flexibility of multidrug efflux pumps MdtB and MdtF.
Authors: Surekha Padmanaban / Clayton Fernando Rencilin / Rupam Biswas / Somnath Dutta /
Abstract: Resistance-nodulation-cell division (RND) efflux pumps are the major cause of multidrug resistance in bacteria, particularly in Gram-negative bacteria. They are complex molecular machines forming ...Resistance-nodulation-cell division (RND) efflux pumps are the major cause of multidrug resistance in bacteria, particularly in Gram-negative bacteria. They are complex molecular machines forming tripartite assemblies that actively transport out a wide range of antimicrobial agents, including antibiotics, biocides, and host defense molecules. However, the presence of multiple RND transporters with overlapping functions in a single bacterium raises questions about their individual functional relevance. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of two distinct hydrophobic and amphiphilic efflux (HAE)-RND transporters from MdtB and MdtF. MdtB transporter is a part of the two-RND subunit system MdtABC. MdtF is a unique class of RND transporter whose expression is regulated by oxygen availability and is crucial for the survival of in anaerobic growth conditions. The cryo-EM structures of MdtB and MdtF reveal a novel conformational state of HAE-RND efflux pumps. While the MdtB structure adopts an intermediate state, MdtF displays structural dynamics in the presence of n-dodecyl-β-D-maltoside (DDM). MdtF at 2.8 Å resolution displayed a significant conformational change in the transmembrane core helices and flexibility in the transmembrane domain. Our findings highlight the significance of the novel structural state during the substrate transport mechanism. Furthermore, our structural analysis provides insights into drug-binding sites and the transport mechanism of these important transporters.
IMPORTANCE: Resistance-nodulation-cell division (RND) efflux pumps are mainly responsible for multidrug resistance by extruding a wide range of antibiotics from bacterial cells. These pumps are ...IMPORTANCE: Resistance-nodulation-cell division (RND) efflux pumps are mainly responsible for multidrug resistance by extruding a wide range of antibiotics from bacterial cells. These pumps are frequently overexpressed in multidrug-resistant strains, which are responsible for urinary tract infections and foodborne illnesses. In this current study, we resolved the structures of two hydrophobic and amphiphilic efflux (HAE)-RND transporters, MdtB and MdtF, using single-particle cryo-electron microscopy. Our study demonstrated novel structural states of MdtF during substrate transport. This knowledge provides valuable insights into the conformational transitions underlying substrate transport. Understanding these structural mechanisms fills a critical knowledge gap in the RND-mediated efflux process and lays the groundwork for structure-guided inhibitor design. Our findings contribute to ongoing efforts to develop novel therapeutic strategies to combat multidrug-resistant infections.
History
DepositionFeb 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Multidrug resistance protein MdtF
D: Multidrug resistance protein MdtF
E: Multidrug resistance protein MdtF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,3076
Polymers334,7753
Non-polymers1,5323
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Multidrug resistance protein MdtF


Mass: 111591.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mdtF, yhiV, b3514, JW3482 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37637
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
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: Membrane protein MdtF / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: OTHER / Num. of particles: 250000 / Symmetry type: POINT

+
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