[English] 日本語
Yorodumi
- PDB-5o66: Asymmetric AcrABZ-TolC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o66
TitleAsymmetric AcrABZ-TolC
Components
  • Multidrug efflux pump accessory protein AcrZ
  • Multidrug efflux pump subunit AcrA
  • Multidrug efflux pump subunit AcrB
  • Outer membrane protein TolC
KeywordsMEMBRANE PROTEIN / multidrug efflux pump / membrane transporter
Function / homology
Function and homology information


MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / xenobiotic transmembrane transporter activity ...MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion channel activity / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding / plasma membrane
Similarity search - Function
Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / Type I secretion outer membrane protein, TolC / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein ...Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump-associated protein AcrZ / Type I secretion outer membrane protein, TolC / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / Outer membrane efflux protein / Outer membrane efflux protein / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Outer membrane protein TolC / Multidrug efflux pump accessory protein AcrZ / Multidrug efflux pump subunit AcrA / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
Escherichia coli O157:H7 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsDu, D. / Luisi, B.F.
Funding support United Kingdom, Japan, 2items
OrganizationGrant numberCountry
Wellcome TrustRG61065 United Kingdom
HFSPRG68784 Japan
CitationJournal: Elife / Year: 2017
Title: An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Authors: Zhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du /
Abstract: Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell ...Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.
History
DepositionJun 5, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJun 14, 2017ID: 5V78
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: em_image_scans / pdbx_validate_close_contact / struct_conn
Revision 1.2Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8640
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein TolC
B: Outer membrane protein TolC
C: Outer membrane protein TolC
D: Multidrug efflux pump subunit AcrA
E: Multidrug efflux pump subunit AcrA
F: Multidrug efflux pump subunit AcrA
G: Multidrug efflux pump subunit AcrA
H: Multidrug efflux pump subunit AcrA
I: Multidrug efflux pump subunit AcrA
J: Multidrug efflux pump subunit AcrB
K: Multidrug efflux pump subunit AcrB
L: Multidrug efflux pump subunit AcrB
M: Multidrug efflux pump accessory protein AcrZ
N: Multidrug efflux pump accessory protein AcrZ
O: Multidrug efflux pump accessory protein AcrZ


Theoretical massNumber of molelcules
Total (without water)759,13515
Polymers759,13515
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Protein Outer membrane protein TolC / Multidrug efflux pump subunit TolC / Outer membrane factor TolC


Mass: 53783.355 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria)
Gene: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
Production host: Escherichia coli (E. coli) / References: UniProt: P02930
#2: Protein
Multidrug efflux pump subunit AcrA / AcrAB-TolC multidrug efflux pump subunit AcrA / Acriflavine resistance protein A


Mass: 39800.660 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: acrA, Z0578, ECs0516 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE07
#3: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113665.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#4: Protein Multidrug efflux pump accessory protein AcrZ / AcrAB-TolC multidrug efflux pump accessory protein AcrZ / Acridine resistance protein Z


Mass: 5995.157 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: acrZ, Z0932, ECs0790 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAX1

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1AcrABZ-TolCCOMPLEXall0MULTIPLE SOURCES
2AcrABZ-TolCCOMPLEX#1, #31RECOMBINANT
3AcrABZ-TolCCOMPLEX#2, #41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli K12 (bacteria)83333
33Escherichia coli O157:H7 (bacteria)83334
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26950 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00875398
ELECTRON MICROSCOPYf_angle_d0.981125159
ELECTRON MICROSCOPYf_dihedral_angle_d11.52446447
ELECTRON MICROSCOPYf_chiral_restr0.0498126
ELECTRON MICROSCOPYf_plane_restr0.00512235

+
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