[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleAn allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Journal, issue, pagesElife, Vol. 6, Year 2017
Publish dateMar 29, 2017
AuthorsZhao Wang / Guizhen Fan / Corey F Hryc / James N Blaza / Irina I Serysheva / Michael F Schmid / Wah Chiu / Ben F Luisi / Dijun Du /
PubMed AbstractBacterial 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.
External linksElife / PubMed:28355133 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.2 - 6.5 Å
Structure data

3636

5ng5

EMDB-3636, PDB-5ng5:
multi-drug efflux; membrane transport; RND superfamily; Drug resistance
Method: EM (single particle) / Resolution: 6.5 Å

8636

5v5s

EMDB-8636, PDB-5v5s:
multi-drug efflux; membrane transport; RND superfamily; Drug resistance
Method: EM (single particle) / Resolution: 6.5 Å

8640

5o66

EMDB-8640: Asymmetric structure of AcrAB-TolC tripartite multi drug efflux pump
PDB-5o66: Asymmetric AcrABZ-TolC
Method: EM (single particle) / Resolution: 5.9 Å

PDB-5nc5:
Crystal structure of AcrBZ in complex with antibiotic puromycin
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

Chemicals

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

ChemComp-D12:
DODECANE

ChemComp-D10:
DECANE

ChemComp-DD9:
nonane

ChemComp-PUY:
PUROMYCIN / antibiotic, inhibitor*YM

ChemComp-HEX:
HEXANE

ChemComp-HOH:
WATER

ChemComp-5QF:
6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile

Source
  • escherichia coli (E. coli)
  • Escherichia coli
  • escherichia coli k12 (bacteria)
  • Escherichia coli (strain K12) (bacteria)
  • escherichia coli k-12 (bacteria)
  • escherichia coli o157:h7 (bacteria)
KeywordsTRANSPORT PROTEIN / Membrane transporter / Multidrug efflux pump / MEMBRANE PROTEIN / multi-drug efflux; membrane transport; RND superfamily; Drug resistance / multi-drug efflux / membrane transport / RND superfamily / Drug resistance

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more