[English] 日本語
Yorodumi
- EMDB-50335: Single particle cryo-EM maps of OqxB monomer classes in salipro n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50335
TitleSingle particle cryo-EM maps of OqxB monomer classes in salipro nanodiscs
Map dataMonomer class 1
Sample
  • Complex: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
    • Protein or peptide: Efflux pump membrane transporter OqxB
KeywordsDrug efflux / RND transporter / TRANSPORT 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 speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsLazarova M / Frangakis A / Pos KM
Funding support Switzerland, Germany, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation3100A0_118402 Switzerland
German Research Foundation (DFG)SFB807-P18 Germany
German Research Foundation (DFG)SFB1507-P3 Germany
German Research Foundation (DFG)DFG-EXC115 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity.
Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay ...Authors: Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay Diederichs / Achilleas S Frangakis / Klaas M Pos /
Abstract: Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of ...Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues and show that the transfer of a single conserved residue between both clusters affects the resistance phenotype not only due to changes in the physicochemical properties of the binding pocket, but also due to an altered equilibrium between the conformational states of the transport cycle. We demonstrate, using single-particle cryo-electron microscopy, that AcrB and OqxB, which represent both clusters, adopt fundamentally different apo states, implying distinct mechanisms for initial substrate binding. The observed conformational plasticity appears phylogenetically conserved and likely plays a role in the diversification of the resistance phenotype among homologous RND pumps.
History
DepositionMay 17, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50335.png

Downloads & links

-
Map

FileDownload / File: emd_50335.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonomer class 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å		0.84 Å/pix.
x 380 pix.
= 318.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.26522496 - 0.5253753
Average (Standard dev.)0.000602052 (±0.010313273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 318.06 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Monomer class 5

Fileemd_50335_additional_1.map
AnnotationMonomer class 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Monomer class 6

Fileemd_50335_additional_2.map
AnnotationMonomer class 6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Monomer class 2

Fileemd_50335_additional_3.map
AnnotationMonomer class 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Monomer class 3

Fileemd_50335_additional_4.map
AnnotationMonomer class 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Monomer class 4

Fileemd_50335_additional_5.map
AnnotationMonomer class 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Monomer class 1 half map

Fileemd_50335_half_map_1.map
AnnotationMonomer class 1 half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Monomer class 1 half map

Fileemd_50335_half_map_2.map
AnnotationMonomer class 1 half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB

EntireName: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
Components
  • Complex: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
    • Protein or peptide: Efflux pump membrane transporter OqxB

-
Supramolecule #1: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB

SupramoleculeName: Trimeric Klebsiella pneumoniae efflux pump membrane transporter OqxB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 343 KDa

-
Macromolecule #1: Efflux pump membrane transporter OqxB

MacromoleculeName: Efflux pump membrane transporter OqxB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFSRFFIDR PIFAAVLSIL IFITGLIAIP LLPVSEYPDV VPPSVQVRAE YPGANPKVIA ETVATPLEEA INGVENMMYM KSVAGSDGV LVTTVTFRPG TDPDQAQVQV QNRVAQAEAR LPEDVRRLGI TTQKQSPTLT LVVHLFSPNG KYDSLYMRNY A TLKVKDEL ...String:
MDFSRFFIDR PIFAAVLSIL IFITGLIAIP LLPVSEYPDV VPPSVQVRAE YPGANPKVIA ETVATPLEEA INGVENMMYM KSVAGSDGV LVTTVTFRPG TDPDQAQVQV QNRVAQAEAR LPEDVRRLGI TTQKQSPTLT LVVHLFSPNG KYDSLYMRNY A TLKVKDEL ARLPGVGQIQ IFGSGEYAMR VWLDPNKVAA RGLTASDVVT AMQEQNVQVS AGQLGAEPLP QESDFLISIN AQ GRLHTEE EFGNIILKTA QDGSLVRLRD VARIEMGSGS YALRSQLNNK DAVGIGIFQS PGANAIDLSN AVRAKMAELA TRF PEDMQW AAPYDPTVFV RDSIRAVVQT LLEAVVLVVL VVILFLQTWR ASIIPLIAVP VSVVGTFSIL YLLGFSLNTL SLFG LVLAI GIVVDDAIVV VENVERNIEE GLAPLAAAHQ AMREVSGPII AIALVLCAVF VPMAFLSGVT GQFYKQFAVT IAIST VISA INSLTLSPAL AALLLKPHGA KKDLPTRLID RLFGWIFRPF NRFFLRSSNG YQGLVSKTLG RRGAVFAVYL LLLCAA GVM FKVVPGGFIP TQDKLYLIGG VKMPEGSSLA RTDAVIRKMS EIGMNTEGVD YAVAFPGLNA LQFTNTPNTG TVFFGLK PF DQRKHTAAEI NAEINAKIAQ IQQGFGFSIL PPPILGLGQG SGYSLYIQDR GGLGYGALQS AVNAMSGAIM QTPGMHFP I STYQANVPQL DVQVDRDKAK AQGVSLTELF GTLQTYLGSS YVNDFNQFGR TWRVMAQADG PYRESVEDIA NLRTRNNQG EMVPIGSMVN ISTTYGPDPV IRYNGYPAAD LIGDADPRVL SSSQAMTHLE ELSKQILPNG MNIEWTDLSF QQATQGNTAL IVFPVAVLL AFLVLAALYE SWTLPLAVIL IVPMTMLSAL FGVWLTGGDN NVFVQVGLVV LMGLACKNAI LIVEFARELE I QGKGIMEA ALEACRLRLR PIVMTSIAFI AGTIPLILGH GAGAEVRGVT GITVFSGMLG VTLFGLFLTP VFYVTLRKLV TR RKPVQED LPAHHHHHH

UniProtKB: Efflux pump membrane transporter

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6562 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1303415
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241017
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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