[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleA structural framework for unidirectional transport by a bacterial ABC exporter.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 117, Issue 32, Page 19228-19236, Year 2020
Publish dateAug 11, 2020
AuthorsChengcheng Fan / Jens T Kaiser / Douglas C Rees /
PubMed AbstractThe ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer ...The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from (Atm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the Atm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As Atm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by Atm1. One of the disulfide crosslinked Atm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.
External linksProc Natl Acad Sci U S A / PubMed:32703810 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.03 - 3.88 Å
Structure data

21356

6vqt

EMDB-21356, PDB-6vqt:
Structure of a bacterial Atm1-family ABC exporter with MgADPVO4 bound
Method: EM (single particle) / Resolution: 3.03 Å

21357

6vqu

EMDB-21357, PDB-6vqu:
Structure of a bacterial Atm1-family ABC exporter
Method: EM (single particle) / Resolution: 3.88 Å

PDB-6pam:
Structure of a bacterial Atm1-family ABC transporter with MgADP bound
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-6pan:
Structure of a bacterial Atm1-family ABC exporter with ATP bound
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

PDB-6pao:
Structure of a bacterial Atm1-family ABC exporter with ATP bound
Method: X-RAY DIFFRACTION / Resolution: 3.65 Å

PDB-6paq:
Structure of a bacterial Atm1-family ABC exporter with ATP bound
Method: X-RAY DIFFRACTION / Resolution: 3.301 Å

PDB-6par:
Structure of a bacterial Atm1-family ABC exporter with MgAMPPNP bound
Method: X-RAY DIFFRACTION / Resolution: 3.35 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-VO4:
VANADATE ION

Source
  • Novosphingobium aromaticivorans DSM 12444 (bacteria)
  • novosphingobium aromaticivorans (strain atcc 700278 / dsm 12444 / cip 105152 / nbrc 16084 / f199) (bacteria)
KeywordsTRANSPORT PROTEIN / ABC transporter / ABC exporter / ATPase / membrane protein

+
About EMN 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

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.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

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more