Structure of a bacterial Atm1-family ABC exporter with MgAMPPNP bound

Experimental Data Snapshot

  • Resolution: 3.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

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This is version 1.3 of the entry. See complete history


A structural framework for unidirectional transport by a bacterial ABC exporter.

Fan, C.Kaiser, J.T.Rees, D.C.

(2020) Proc Natl Acad Sci U S A 117: 19228-19236

  • DOI: https://doi.org/10.1073/pnas.2006526117
  • Primary Citation of Related Structures:  
    6PAM, 6PAN, 6PAO, 6PAQ, 6PAR, 6VQT, 6VQU

  • PubMed Abstract: 

    The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans ( Na Atm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the Na 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 Na 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 4 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 Na Atm1. One of the disulfide crosslinked Na 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.

  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATM1-type heavy metal exporter
A, B, C, D, E
A, B, C, D, E, F
614Novosphingobium aromaticivorans DSM 12444Mutation(s): 0 
Gene Names: atm1Saro_2631
Membrane Entity: Yes 
Find proteins for Q2G506 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199))
Explore Q2G506 
Go to UniProtKB:  Q2G506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G506
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ANP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
C10 H17 N6 O12 P3
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.648α = 90
b = 92.498β = 110.34
c = 237.691γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection

Structure Validation

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Ligand Structure Quality Assessment 

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: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-08-26
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description