[English] 日本語
Yorodumi
- EMDB-53281: Single particle cryo-EM structure of the multidrug efflux pump Md... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53281
TitleSingle particle cryo-EM structure of the multidrug efflux pump MdtF from Escherichia coli
Map data
Sample
  • Complex: Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc
    • Protein or peptide: Multidrug resistance protein MdtF
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: DODECANE
Keywordsmultidrug / pump / anaerobic / lipid / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsLawrence R / Adams C / Sousa JS / Ahdash Z / Reading E
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008709/1 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Molecular basis for multidrug efflux by an anaerobic RND transporter.
Authors: Ryan Lawrence / Mohd Athar / Muhammad R Uddin / Christopher Adams / Joana S Sousa / Oliver Durrant / Sophie Lellman / Lucy Sutton / C William Keevil / Nisha Patel / Christine Prosser / David ...Authors: Ryan Lawrence / Mohd Athar / Muhammad R Uddin / Christopher Adams / Joana S Sousa / Oliver Durrant / Sophie Lellman / Lucy Sutton / C William Keevil / Nisha Patel / Christine Prosser / David McMillan / Helen I Zgurskaya / Attilio V Vargiu / Zainab Ahdash / Eamonn Reading
Abstract: Bacteria can resist antibiotics and toxic substances within demanding ecological settings, such as low oxygen, extreme acid, and during nutrient starvation. MdtEF, a proton motive force-driven efflux ...Bacteria can resist antibiotics and toxic substances within demanding ecological settings, such as low oxygen, extreme acid, and during nutrient starvation. MdtEF, a proton motive force-driven efflux pump from the resistance-nodulation-cell division (RND) superfamily, is upregulated in these conditions but its molecular mechanism is unknown. Here, we report cryo-electron microscopy structures of Escherichia coli multidrug transporter MdtF within native-lipid nanodiscs, including a single-point mutant with an altered multidrug phenotype and associated substrate-bound form. We reveal that drug binding domain and channel conformational plasticity likely governs promiscuous substrate specificity, analogous to its closely related, constitutively expressed counterpart, AcrB. Whereas we discover distinct transmembrane state transitions within MdtF, which create a more engaged proton relay network, altered drug transport allostery and an acid-responsive increase in efflux efficiency. Physiologically, this provides means of xenobiotic and metabolite disposal within remodelled cell membranes that presage encounters with acid stresses, as endured in the gastrointestinal tract.
History
DepositionMar 28, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53281.png

Downloads & links

-
Map

FileDownload / File: emd_53281.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 260 pix.
= 245.96 Å		0.95 Å/pix.
x 260 pix.
= 245.96 Å		0.95 Å/pix.
x 260 pix.
= 245.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.13453828 - 0.20933744
Average (Standard dev.)0.00013761078 (±0.0081608035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 245.95999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_53281_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53281_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc

EntireName: Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc
Components
  • Complex: Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc
    • Protein or peptide: Multidrug resistance protein MdtF
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: DODECANE

-
Supramolecule #1: Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc

SupramoleculeName: Homotrimer of WT multidrug resistance protein MdtF in SMALP nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 334.551 KDa

-
Macromolecule #1: Multidrug resistance protein MdtF

MacromoleculeName: Multidrug resistance protein MdtF / type: protein_or_peptide / ID: 1
Details: MdtF protein with a C-terminal 6x His (hexahistidine) tag, separated by a linker sequence including a TEV cleavage site
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 113.759867 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MANYFIDRPV FAWVLAIIMM LAGGLAIMNL PVAQYPQIAP PTITVSATYP GADAQTVEDS VTQVIEQNMN GLDGLMYMSS TSDAAGNAS ITLTFETGTS PDIAQVQVQN KLQLAMPSLP EAVQQQGISV DKSSSNILMV AAFISDNGSL NQYDIADYVA S NIKDPLSR ...String:
MANYFIDRPV FAWVLAIIMM LAGGLAIMNL PVAQYPQIAP PTITVSATYP GADAQTVEDS VTQVIEQNMN GLDGLMYMSS TSDAAGNAS ITLTFETGTS PDIAQVQVQN KLQLAMPSLP EAVQQQGISV DKSSSNILMV AAFISDNGSL NQYDIADYVA S NIKDPLSR TAGVGSVQLF GSEYAMRIWL DPQKLNKYNL VPSDVISQIK VQNNQISGGQ LGGMPQAADQ QLNASIIVQT RL QTPEEFG KILLKVQQDG SQVLLRDVAR VELGAEDYST VARYNGKPAA GIAIKLAAGA NALDTSRAVK EELNRLSAYF PAS LKTVYP YDTTPFIEIS IQEVFKTLVE AIILVFLVMY LFLQNFRATI IPTIAVPVVI LGTFAILSAV GFTINTLTMF GMVL AIGLL VDDAIVVVEN VERVIAEDKL PPKEATHKSM GQIQRALVGI AVVLSAVFMP MAFMSGATGE IYRQFSITLI SSMLL SVFV AMSLTPALCA TILKAAPEGG HKPNALFARF NTLFEKSTQH YTDSTRSLLR CTGRYMVVYL LICAGMAVLF LRTPTS FLP EEDQGVFMTT AQLPSGATMV NTTKVLQQVT DYYLTKEKDN VQSVFTVGGF GFSGQGQNNG LAFISLKPWS ERVGEEN SV TAIIQRAMIA LSSINKAVVF PFNLPAVAEL GTASGFDMEL LDNGNLGHEK LTQARNELLS LAAQSPNQVT GVRPNGLE D TPMFKVNVNA AKAEAMGVAL SDINQTISTA FGSSYVNDFL NQGRVKKVYV QAGTPFRMLP DNINQWYVRN ASGTMAPLS AYSSTEWTYG SPRLERYNGI PSMEILGEAA AGKSTGDAMK FMADLVAKLP AGVGYSWTGL SYQEALSSNQ APALYAISLV VVFLALAAL YESWSIPFSV MLVVPLGVVG ALLATDLRGL SNDVYFQVGL LTTIGLSAKN AILIVEFAVE MMQKEGKTPI E AIIEAARM RLRPILMTSL AFILGVLPLV ISHGAGSGAQ NAVGTGVMGG MFAATVLAIY FVPVFFVVVE HLFARFKKAA SG ENLYFQS LEHHHHHH

UniProtKB: Multidrug resistance protein MdtF

-
Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 21 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Macromolecule #3: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 3 / Number of copies: 7 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.82 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000

+
Image processing

Particle selectionNumber selected: 2501990
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

24653

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 583735
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9qpr:
Single particle cryo-EM structure of the multidrug efflux pump MdtF from Escherichia coli

+
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