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- PDB-6vqu: Structure of a bacterial Atm1-family ABC exporter -

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Basic information

Database: PDB / ID: 6vqu
TitleStructure of a bacterial Atm1-family ABC exporter
ComponentsATM1-type heavy metal exporter
KeywordsTRANSPORT PROTEIN / ABC transporter / membrane protein
Function / homology
Function and homology information

response to mercury ion / ATPase-coupled transmembrane transporter activity / ion transport / ATPase activity / integral component of membrane / ATP binding / plasma membrane
AAA+ ATPase domain / ABC transporter-like / ABC transporter type 1, transmembrane domain / ABC transporter, conserved site / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily / Type I protein exporter
ATM1-type heavy metal exporter
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsFan, C. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2020
Title: A structural framework for unidirectional transport by a bacterial ABC exporter.
Authors: Chengcheng Fan / Jens T Kaiser / Douglas C Rees /
Abstract: 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 ...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.
Validation Report
SummaryFull reportAbout validation report
DepositionFeb 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

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Deposited unit
A: ATM1-type heavy metal exporter
B: ATM1-type heavy metal exporter

Theoretical massNumber of molelcules
Total (without water)135,5432

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein ATM1-type heavy metal exporter / ATP-binding cassette transporter Atm1 / NaAtm1

Mass: 67771.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Gene: atm1, Saro_2631 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G506

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

ComponentName: homodimeric Atm1-type heavy metal transporter / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.133 MDa / Experimental value: NO
Source (natural)Organism: Novosphingobium aromaticivorans DSM 12444 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
1100 mMSodium ChlorideNaClSodium chloride1
220 mMTrisTris1
SpecimenConc.: 4 mg/ml
Details: The sample was reconstituted with MSP1D1 nanodiscs and POPC.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
2EPUimage acquisition
4CTFFINDCTF correction
7PHENIX1.17.1model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13PHENIX1.17.1model refinement
Particle selectionNum. of particles selected: 1145444
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102076 / Symmetry type: POINT
Atomic model buildingB value: 23 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4MRN
Pdb chain-ID: A
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0079326
ELECTRON MICROSCOPYf_angle_d0.88212668
ELECTRON MICROSCOPYf_dihedral_angle_d8.7741306
ELECTRON MICROSCOPYf_chiral_restr0.0561484
ELECTRON MICROSCOPYf_plane_restr0.0071616

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