[English] 日本語
Yorodumi
- EMDB-47796: Pseudomonas aeruginosa MexY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47796
TitlePseudomonas aeruginosa MexY
Map data
Sample
  • Complex: MexY
    • Protein or peptide: Efflux pump membrane transporter
KeywordsPseudomonsa aeruginosa / MexY / RND / Efflux / MEMBRANE PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / response to toxic substance / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsGregor WD / Maharjan R / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145069 United States
CitationJournal: mBio / Year: 2025
Title: Cryo-EM structure of the MexY multidrug efflux pump.
Authors: William D Gregor / Rakesh Maharjan / Zhemin Zhang / Lucius Chiaraviglio / Nithya Sastry / Meng Cui / James E Kirby / Edward W Yu /
Abstract: , a Gram-negative pathogen, has emerged as one of the most highly antibiotic-resistant bacteria worldwide and subsequently has become a leading cause of healthcare-associated, life-threatening ..., a Gram-negative pathogen, has emerged as one of the most highly antibiotic-resistant bacteria worldwide and subsequently has become a leading cause of healthcare-associated, life-threatening infections. multidrug efflux Y (MexY) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. It is a major determinant for resistance to aminoglycosides in this opportunistic pathogen. However, the detailed molecular mechanisms involved in aminoglycoside recognition and extrusion by MexY have not been elucidated. Here, we report the cryo-electron microscopy structure of MexY to a resolution of 3.63 Å. The structure directly indicates two plausible pathways for drug export. It also suggests that MexY is capable of picking up antibiotics via the ceiling of the central cavity formed by the MexY trimer. Molecular dynamics simulations depict that MexY is able to use a tunnel connecting the central cavity to the funnel of the trimer to export its substrates.
IMPORTANCE: Here, we report the cryo-electron microscopy structure of the MexY multidrug efflux pump, posing the possibility that this pump is capable of capturing antibiotics from both the central ...IMPORTANCE: Here, we report the cryo-electron microscopy structure of the MexY multidrug efflux pump, posing the possibility that this pump is capable of capturing antibiotics from both the central cavity and the periplasmic cleft of the pump. The results indicate that MexY may utilize charged residues to bind and export drugs, mediating resistance to these antibiotics.
History
DepositionNov 8, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47796.png

Downloads & links

-
Map

FileDownload / File: emd_47796.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3587196 - 0.68962556
Average (Standard dev.)-0.00021524368 (±0.028674109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_47796_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47796_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MexY

EntireName: MexY
Components
  • Complex: MexY
    • Protein or peptide: Efflux pump membrane transporter

-
Supramolecule #1: MexY

SupramoleculeName: MexY / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

-
Macromolecule #1: Efflux pump membrane transporter

MacromoleculeName: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 111.287914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARFFIDRPV FAWVISLLIV LAGVLAIRFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASL TLTFRQGVNA DLAAVEVQNR LKIVESRLPE SVRRDGIYVE KAADSIQLIV TLTSSSGRYD AMELGEIASS N VLQALRRV ...String:
MARFFIDRPV FAWVISLLIV LAGVLAIRFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASL TLTFRQGVNA DLAAVEVQNR LKIVESRLPE SVRRDGIYVE KAADSIQLIV TLTSSSGRYD AMELGEIASS N VLQALRRV EGVGKVETWG AEYAMRIWPD PAKLTSMNLS ASDLVNAVRR HNARLTVGDI GNLGVPDSAP ISATVKVDDT LV TPEQFGE IPLRIRADGG AIRLRDVARV EFGQSEYGFV SRVNQMTATG LAVKMAPGSN AVATAKRIRA TLDELSRYFP EGV SYNIPY DTSAFVEISI RKVVSTLLEA MLLVFAVMYL FMQNFRATLI PTLVVPVALL GTFTVMLGLG FSINVLTMFG MVLA IGILV DDAIIVVENV ERLMAEEGLS PHDATVKAMR QISGAIVGIT VVLVSVFVPM AFFSGAVGNI YRQFAVTLAV SIGFS AFLA LSLTPALCAT LLRPIDADHH EKRGFFGWFN RAFLRLTGRY RNAVAGILAR PIRWMLVYAL VIGVVALLFV RLPQAF LPE EDQGDFMIMV MQPEGTPMAE TMANVGDVER YLAEHEPVAY AYAVGGFSLY GDGTSSAMIF ATLKDWSERR EASQHVG AI VERINQRFAG LPNRTVYAMN SPPLPDLGST SGFDFRLQDR GGVGYEALVK ARDQLLARAA EDPRLANVMF AGQGEAPQ I RLDIDRRKAE TLGVSMDEIN TTLAVMFGSD YIGDFMHGSQ VRKVVVQADG AKRLGIDDIG RLHVRNEQGE MVPLATFAK AAWTLGPPQL TRYNGYPSFN LEGQAAPGYS SGEAMQAMEQ LMQGLPEGIA HEWSGQSFEE RLSGAQAPAL FALSVLIVFL ALAALYESW SIPLAVILVV PLGVLGALLG VSLRGLPNDI YFKVGLITII GLSAKNAILI IEVAKDHYQE GMSLLQATLE A ARLRLRPI VMTSLAFGFG VVPLALSSGA GSGAQVAIGT GVLGGIVTAT VLAVFLVPLF FLVVGRLFRL RKA

UniProtKB: Efflux pump membrane transporter

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris HCl
100.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2124205
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8886
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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