4MRS

Structure of a bacterial Atm1-family ABC transporter

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Literature

Structural basis for heavy metal detoxification by an Atm1-type ABC exporter.

Lee, J.Y., Yang, J.G., Zhitnitsky, D., Lewinson, O., Rees, D.C.

(2014) Science 343: 1133-1136

  • DOI: 10.1126/science.1246489
  • Primary Citation of Related Structures:  
    4MRN, 4MRP, 4MRR, 4MRS, 4MRV

  • PubMed Abstract: 

    • Although substantial progress has been achieved in the structural analysis of exporters from the superfamily of adenosine triphosphate (ATP)-binding cassette (ABC) transporters, much less is known about how they selectively recognize substrates and how substrate binding is coupled to ATP hydrolysis ...

    Although substantial progress has been achieved in the structural analysis of exporters from the superfamily of adenosine triphosphate (ATP)-binding cassette (ABC) transporters, much less is known about how they selectively recognize substrates and how substrate binding is coupled to ATP hydrolysis. We have addressed these questions through crystallographic analysis of the Atm1/ABCB7/HMT1/ABCB6 ortholog from Novosphingobium aromaticivorans DSM 12444, NaAtm1, at 2.4 angstrom resolution. Consistent with a physiological role in cellular detoxification processes, functional studies showed that glutathione derivatives can serve as substrates for NaAtm1 and that its overexpression in Escherichia coli confers protection against silver and mercury toxicity. The glutathione binding site highlights the articulated design of ABC exporters, with ligands and nucleotides spanning structurally conserved elements to create adaptable interfaces accommodating conformational rearrangements during the transport cycle.

    Organizational Affiliation: 

    Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC transporter related proteinA, B614Novosphingobium aromaticivorans DSM 12444Mutation(s): 0 
Gene Names: atm1, Saro_2631
EC: 7
Membrane Entity: Yes 
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDS
Query on GDS
Download Ideal Coordinates CCD File 
E [auth A],
O [auth B]		OXIDIZED GLUTATHIONE DISULFIDE
C20 H32 N6 O12 S2
YPZRWBKMTBYPTK-BJDJZHNGSA-N		 Ligand Interaction
LDA
Query on LDA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth A],
I [auth A],
J [auth A],
C [auth A],
D [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
P [auth B],
Q [auth B]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 322.173α = 90
b = 95.401β = 101.81
c = 79.398γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description