[English] 日本語
Yorodumi
- EMDB-40179: Multi-drug efflux pump RE-CmeB bound with Chloramphenicol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40179
TitleMulti-drug efflux pump RE-CmeB bound with Chloramphenicol
Map dataMulti-drug efflux pump RE-CmeB bound with Chloramphenicol
Sample
  • Complex: RE-CmeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: CHLORAMPHENICOL
Keywordsefflux pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


xenobiotic transport / efflux transmembrane transporter activity / plasma membrane
Similarity search - Function
Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsZhang Z
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: Microbiol Spectr / Year: 2023
Title: Cryo-Electron Microscopy Structures of a Campylobacter Multidrug Efflux Pump Reveal a Novel Mechanism of Drug Recognition and Resistance.
Authors: Zhemin Zhang / Nicholas Lizer / Zuowei Wu / Christopher E Morgan / Yuqi Yan / Qijing Zhang / Edward W Yu /
Abstract: Campylobacter jejuni is a bacterium that is commonly present in the intestinal tracts of animals. It is also a major foodborne pathogen that causes gastroenteritis in humans. The most predominant and ...Campylobacter jejuni is a bacterium that is commonly present in the intestinal tracts of animals. It is also a major foodborne pathogen that causes gastroenteritis in humans. The most predominant and clinically important multidrug efflux system in C. jejuni is the CmeABC (Campylobacter multidrug efflux) pump, a tripartite system that includes an inner membrane transporter (CmeB), a periplasmic fusion protein (CmeA), and an outer membrane channel protein (CmeC). This efflux protein machinery mediates resistance to a number of structurally diverse antimicrobial agents. A recently identified CmeB variant, termed resistance enhancing CmeB (RE-CmeB), can increase its multidrug efflux pump activity, likely by influencing antimicrobial recognition and extrusion. Here, we report structures of RE-CmeB in its apo form as well as in the presence of four different drugs by using single-particle cryo-electron microscopy (cryo-EM). Coupled with mutagenesis and functional studies, this structural information allows us to identify critical amino acids that are important for drug resistance. We also report that RE-CmeB utilizes a somewhat unique subset of residues to bind different drugs, thereby optimizing its ability to accommodate different compounds with distinct scaffolds. These findings provide insights into the structure-function relationship of this newly emerged antibiotic efflux transporter variant in Campylobacter. Campylobacter jejuni has emerged as one of the most problematic and highly antibiotic-resistant pathogens, worldwide. The Centers for Disease Control and Prevention have designated antibiotic-resistant C. jejuni as a serious antibiotic resistance threat in the United States. We recently identified a C. jejuni resistance enhancing CmeB (RE-CmeB) variant that can increase its multidrug efflux pump activity and confers an exceedingly high-level of resistance to fluoroquinolones. Here, we report the cryo-EM structures of this prevalent and clinically important C. jejuni RE-CmeB multidrug efflux pump in both the absence and presence of four antibiotics. These structures allow us to understand the action mechanism for multidrug recognition in this pump. Our studies will ultimately inform an era in structure-guided drug design to combat multidrug resistance in these Gram-negative pathogens.
History
DepositionMar 17, 2023-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40179.png

Downloads & links

-
Map

FileDownload / File: emd_40179.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMulti-drug efflux pump RE-CmeB bound with Chloramphenicol
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 Å		1.07 Å/pix.
x 352 pix.
= 376.64 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-0.49197152 - 1.048018
Average (Standard dev.)-0.00010713821 (±0.032689527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map 1

Fileemd_40179_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_40179_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RE-CmeB

EntireName: RE-CmeB
Components
  • Complex: RE-CmeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: CHLORAMPHENICOL

-
Supramolecule #1: RE-CmeB

SupramoleculeName: RE-CmeB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Campylobacter jejuni (Campylobacter)

-
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: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 114.122477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFSKFFIERP IFASVVAIII SIAGIIGLAN LPVEQYPSLT PPTVQVSATY TGADAQTIAS TVATPIEDAI NGVDNMIYMD STSSPGQMK LTVYFNIGTD PDQAAIDVNN RISAATAKLP EAVKKLGVTV RKSSSTILEV VSVYSEDSSM NDIDIYNYVS L NILDELKR ...String:
MFSKFFIERP IFASVVAIII SIAGIIGLAN LPVEQYPSLT PPTVQVSATY TGADAQTIAS TVATPIEDAI NGVDNMIYMD STSSPGQMK LTVYFNIGTD PDQAAIDVNN RISAATAKLP EAVKKLGVTV RKSSSTILEV VSVYSEDSSM NDIDIYNYVS L NILDELKR IPGVGDASAI GNKNYSMRIW LEPDLLNKFG VTANDVINAV NDQNAQYATG KIGEEPVVNK SPQVISITMQ GR LQTPQEF ENIILRVNED KSFLRIKDVA KVEIGAEQYN STGRLNTSAA VPIIINLQSG ANAVNTAKLI NEKMQELSKN FPQ GLKYQI PYDTTIFVKA SIKEVIKTFV EALALVLVVM YLFLKNFKST IIPMIAVPVS LLGTFAVLYV LGFSINLLTL FALV LAIGI VVDDAIIVVE NIDRILHEDS NISVKDAAIK AMNEVSSPVI SIVLVLCAVF IPVSFISGFV GEIQRQFALT LAISV AISG FVALTLTPSL SALFLTRNES KPFYFIQKFN DFFDWSTSVF SSGVAYILKR TIRFVLVFCI MIGFIAYLFK IVPSSL VPS EDQGVIMSII NLPSGSSIHR TIEEVDTINK NATQMKEISS SVSLIGFDLF TSSLKENAAA VFFILKDWSQ REASSDQ II AQLFGQYAAD RNALSYFLNL PPIPGLSLTG GFEMYAQNKS GKDYDAIQQD VNKMLELART RKELANVRTT LDTSFPQY K LIIDRDKMKY YNLNMQDVFN TISATIGTYY VNDFPMLGKN FQVNIRALGD FRNTQDALKN IYIRSSDNKM IPLNSFLTL VRSAGPDDVK RFNLFPAALI QGDPAPGYTS GQAIDAIAEV AKQSLGDEYS IAWSGSAYQE VSSKGAGAYA FVLGMIFVFL ILAAQYERW LMPLAVITAV PFAVFGSILL VALRGFDNDI YFQTGLLLLI GLSAKNAILI IEFAMEERLK KGKSIFEAAI N AAKLRFRP IIMTSLAFTF GVLPMIFATG AGSASRHSLG TGLIGGMIAA STLAIFFVPL FFYLLENFNE WLDKKRGKVH E

UniProtKB: CmeB

-
Macromolecule #2: CHLORAMPHENICOL

MacromoleculeName: CHLORAMPHENICOL / type: ligand / ID: 2 / Number of copies: 1 / Formula: CLM
Molecular weightTheoretical: 323.129 Da
Chemical component information

ChemComp-CLM:
CHLORAMPHENICOL / antibiotic*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.8 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 / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15632
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