7N5B

Structure of AtAtm3 in the outward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Glutathione binding to the plant At Atm3 transporter and implications for the conformational coupling of ABC transporters.

Fan, C.Rees, D.C.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.76140
  • Primary Citation of Related Structures:  
    7N58, 7N59, 7N5A, 7N5B

  • PubMed Abstract: 

    The ATP binding cassette (ABC) transporter of mitochondria (Atm) from Arabidopsis thaliana ( At Atm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by exporting glutathione derivatives. Using single-particle cryo-electron microscopy, we have determined four structures of At Atm3 in three different conformational states: two inward-facing conformations (with and without bound oxidized glutathione [GSSG]), together with closed and outward-facing states stabilized by MgADP-VO 4 . These structures not only provide a structural framework for defining the alternating access transport cycle, but also reveal the paucity of cysteine residues in the glutathione binding site that could potentially form inhibitory mixed disulfides with GSSG. Despite extensive efforts, we were unable to prepare the ternary complex of At Atm3 containing both GSSG and MgATP. A survey of structurally characterized type IV ABC transporters that includes At Atm3 establishes that while nucleotides are found associated with all conformational states, they are effectively required to stabilize occluded, closed, and outward-facing conformations. In contrast, transport substrates have only been observed associated with inward-facing conformations. The absence of structures with dimerized nucleotide binding domains containing both nucleotide and transport substrate suggests that this form of the ternary complex exists only transiently during the transport cycle.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter B family member 25, mitochondrial
A, B
739Arabidopsis thalianaMutation(s): 0 
Gene Names: ABCB25ATM3STA1At5g58270MCK7.14
Membrane Entity: Yes 
UniProt
Find proteins for Q9LVM1 (Arabidopsis thaliana)
Explore Q9LVM1 
Go to UniProtKB:  Q9LVM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LVM1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC2.15

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references