[English] 日本語
Yorodumi
- EMDB-22866: Cryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22866
TitleCryo-EM Structures of AdeB from Acinetobacter baumannii: AdeB-I
Map dataDensity Modified Map of AdeB-I
Sample
  • Complex: AdeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE
KeywordsAdeB / Acinetobacter baumannii / Membrane Protein / Cryo-EM / RND transporter / TRANSPORT PROTEIN
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsMorgan CE / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2021
Title: Cryoelectron Microscopy Structures of AdeB Illuminate Mechanisms of Simultaneous Binding and Exporting of Substrates.
Authors: Christopher E Morgan / Przemyslaw Glaza / Inga V Leus / Anhthu Trinh / Chih-Chia Su / Meng Cui / Helen I Zgurskaya / Edward W Yu /
Abstract: is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic ... is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic pathogens is a major cause of failure of drug-based treatments of infectious diseases. The best-characterized multidrug efflux system in is the prevalent rug fflux B (AdeB) pump, which is a member of the resistance-nodulation-cell division (RND) superfamily. Here, we report six structures of the trimeric AdeB multidrug efflux pump in the presence of ethidium bromide using single-particle cryoelectron microscopy (cryo-EM). These structures allow us to directly observe various novel conformational states of the AdeB trimer, including the transmembrane region of trimeric AdeB can be associated with form a trimer assembly or dissociated into "dimer plus monomer" and "monomer plus monomer plus monomer" configurations. We also discover that a single AdeB protomer can simultaneously anchor a number of ethidium ligands and that different AdeB protomers can bind ethidium molecules simultaneously. Combined with molecular dynamics (MD) simulations, we reveal a drug transport mechanism that involves multiple multidrug-binding sites and various transient states of the AdeB membrane protein. Our data suggest that each AdeB protomer within the trimer binds and exports drugs independently. has emerged as one of the most highly antibiotic-resistant Gram-negative pathogens. The prevalent AdeB multidrug efflux pump mediates resistance to a broad spectrum of clinically relevant antimicrobial agents. Here, we report six cryo-EM structures of the trimeric AdeB pump in the presence of ethidium bromide. We discover that a single AdeB protomer can simultaneously anchor a number of ligands, and different AdeB protomers can bind ethidium molecules simultaneously. The results indicate that each AdeB protomer within the trimer recognizes and extrudes drugs independently.
History
DepositionOct 16, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kgd
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22866.png

Downloads & links

-
Map

FileDownload / File: emd_22866.map.gz / Format: CCP4 / Size: 13 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity Modified Map of AdeB-I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 149 pix.
= 160.92 Å		1.08 Å/pix.
x 149 pix.
= 160.92 Å		1.08 Å/pix.
x 153 pix.
= 165.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-1.5208077 - 1.971955
Average (Standard dev.)-0.000000000000345 (±0.12381083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin102105104
Dimensions149153149
Spacing149149153
CellA: 160.92001 Å / B: 160.92001 Å / C: 165.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z149149153
origin x/y/z0.0000.0000.000
length x/y/z160.920160.920165.240
α/β/γ90.00090.00090.000
start NX/NY/NZ104102105
NX/NY/NZ149149153
MAP C/R/S321
start NC/NR/NS105102104
NC/NR/NS153149149
D min/max/mean-1.5211.972-0.000

-
Supplemental data

-
Sample components

-
Entire : AdeB

EntireName: AdeB
Components
  • Complex: AdeB
    • Protein or peptide: Efflux pump membrane transporter
  • Ligand: PHOSPHATIDYLETHANOLAMINE

-
Supramolecule #1: AdeB

SupramoleculeName: AdeB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (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: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 112.588297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQFFIRRPV FAWVIAIFII IFGLLSIPKL PIARFPSVAP PQVNISATYP GATAKTINDS VVTLIERELS GVKNLLYYSA TTDTSGTAE ITATFKPGTD VEMAQVDVQN KIKAVEARLP QVVRQQGLQV EASSSGFLML VGINSPNNQY SEVDLSDYLV R NVVEELKR ...String:
MSQFFIRRPV FAWVIAIFII IFGLLSIPKL PIARFPSVAP PQVNISATYP GATAKTINDS VVTLIERELS GVKNLLYYSA TTDTSGTAE ITATFKPGTD VEMAQVDVQN KIKAVEARLP QVVRQQGLQV EASSSGFLML VGINSPNNQY SEVDLSDYLV R NVVEELKR VEGVGKVQSF GAEKAMRIWV DPNKLVSYGL SISDVNNAIR ENNVEIAPGR LGDLPAEKGQ LITIPLSAQG QL SSLEQFK NISLKSKTNG SVIKLSDVAN VEIGSQAYNF AILENGKPAT AAAIQLSPGA NAVKTAEGVR AKIEELKLNL PEG MEFSIP YDTAPFVKIS IEKVIHTLLE AMVLVFIVMY LFLHNVRYTL IPAIVAPIAL LGTFTVMLLA GFSINVLTMF GMVL AIGII VDDAIVVVEN VERIMATEGL SPKDATSKAM KEITSPIIGI TLVLAAVFLP MAFASGSVGV IYKQFTLTMS VSILF SALL ALILTPALCA TILKPIDGHH QKKGFFAWFD RSFDKVTKKY ELMLLKIIKH TVPMMVIFLV ITGITFAGMK YWPTAF MPE EDQGWFMTSF QLPSDATAER TRNVVNQFEN NLKDNPDVKS NTAILGWGFS GAGQNVAVAF TTLKDFKERT SSASKMT SD VNSSMANSTE GETMAVLPPA IDELGTFSGF SLRLQDRANL GMPALLAAQD ELMAMAAKNK KFYMVWNEGL PQGDNISL K IDREKLSALG VKFSDVSDII STSMGSMYIN DFPNQGRMQQ VIVQVEAKSR MQLKDILNLK VMGSSGQLVS LSEVVTPQW NKAPQQYNRY NGRPSLSIAG IPNFDTSSGE AMREMEQLIA KLPKGIGYEW TGISLQEKQS ESQMAFLLGL SMLVVFLVLA ALYESWAIP LSVMLVVPLG IFGAIIAIMS RGLMNDVFFK IGLITIIGLS AKNAILIVEF AKMLKEEGMS LIEATVAAAK L RLRPILMT SLAFTCGVIP LVIATGASSE TQHALGTGVF GGMISATILA IFFVPVFFIF ILGAVEKLFS SKKKISS

UniProtKB: Efflux pump membrane transporter

-
Macromolecule #2: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 2 / Number of copies: 6 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 16223
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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