[English] 日本語
Yorodumi
- EMDB-3330: Cryo-electron microscopy structure of AcrBA-TolC-MacA hybrid complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3330
TitleCryo-electron microscopy structure of AcrBA-TolC-MacA hybrid complex
Map dataCryo-electron microscopy single particle analysis 3D reconstruction of AcrBA-TolC-MacA hybrid complex
Sample
  • Sample: AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein
  • Protein or peptide: AcrBA-TolC-MacA hybrid complex
KeywordsMultidrug efflux pump / AcrA / AcrB / TolC / MacA / Resistance-nodulation-division transporter
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsJeong H / Kim J-S / Song S / Shigematsu H / Yokoyama T / Hyun J / Ha N-C
CitationJournal: Structure / Year: 2016
Title: Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC.
Authors: Hyeongseop Jeong / Jin-Sik Kim / Saemee Song / Hideki Shigematsu / Takeshi Yokoyama / Jaekyung Hyun / Nam-Chul Ha /
Abstract: The resistance-nodulation-division type tripartite pump AcrAB-TolC and its homologs are responsible for multidrug resistance in Gram-negative bacteria by expelling a wide variety of toxic substrates. ...The resistance-nodulation-division type tripartite pump AcrAB-TolC and its homologs are responsible for multidrug resistance in Gram-negative bacteria by expelling a wide variety of toxic substrates. The three essential components, AcrA, AcrB, and TolC, must function in concert with each respective binding partner within the complex. In this study, we report an 8.2-Å resolution cryo-electron microscopy (cryo-EM) 3D reconstruction of the complex that consists of an AcrAB fusion protein and a chimeric TolC protein. The pseudoatomic structure derived from the cryo-EM reconstruction clearly demonstrates a model only compatible with the adaptor bridging mechanism, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel-like interaction with the α-barrel tip region of TolC. These observations provide a structural milestone for understanding multidrug resistance in pathogenic Gram-negative bacteria, and may also lead to the design of new antibacterial drugs.
History
DepositionFeb 11, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseMar 9, 2016-
UpdateMar 16, 2016-
Current statusMar 16, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3330.tif

Downloads & links

-
Map

FileDownload / File: emd_3330.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy single particle analysis 3D reconstruction of AcrBA-TolC-MacA hybrid complex
Voxel sizeX=Y=Z: 1.947 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.18344106 - 0.60849404
Average (Standard dev.)0.00237066 (±0.02102367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 467.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.9471.9471.947
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z467.280467.280467.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1830.6080.002

-
Supplemental data

-
Sample components

-
Entire : AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein

EntireName: AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein
Components
  • Sample: AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein
  • Protein or peptide: AcrBA-TolC-MacA hybrid complex

-
Supramolecule #1000: AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein

SupramoleculeName: AcrBA fusion protein in complex with MacA-TolC hybrid dimer protein
type: sample / ID: 1000
Oligomeric state: AcrBA homotrimer in complex with MacA-TolC homotrimer
Number unique components: 1
Molecular weightTheoretical: 650 KDa

-
Macromolecule #1: AcrBA-TolC-MacA hybrid complex

MacromoleculeName: AcrBA-TolC-MacA hybrid complex / type: protein_or_peptide / ID: 1
Details: 3 copies of AcrBA fusion protein in complex with 3 copies of TolC-MacA hybrid dimer
Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 650 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET22b

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES, 150 mM NaCl, and 2 mM b-mercaptoethanol
GridDetails: Holey carbon EM grid (Quantifoil R1.2/1.3)
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV
Method: Blot force 2, Blot time 4 sec, Wait time 30 sec, No drain time, Chamber temperature 4 degrees Celcius

-
Electron microscopy

MicroscopeOTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 71895 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: OTHER
DateApr 4, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 595 / Average electron dose: 24 e/Å2
Details: Every image is the average of seven frames recorded by direct electron detector

-
Image processing

CTF correctionDetails: each particle
Final two d classificationNumber classes: 200
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 20402
DetailsImage processing was performed using Relion 1.3 software. Particles were semi-automatically selected. From 200 class averages, particles that belong in class averages with sharp structural details were used for subsequent 3D classification and refinement. After refinement, B-factor sharpening and MTF correction was performed.

-
Atomic model buiding 1

Initial modelPDB ID:

1iwg

SoftwareName: Chimera, PHENIX, Coot
DetailsExperimental and model structures of AcrB timer, AcrA hexamer and MacA-TolC hybrid dimer were docked into cryo-EM reconstruction as separate rigid bodies. Docking was manually performed using UCSF Chimera and PHENIX, followed by manual adjustments using Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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