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- EMDB-21357: Structure of a bacterial Atm1-family ABC exporter -

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Basic information

Entry
Database: EMDB / ID: EMD-21357
TitleStructure of a bacterial Atm1-family ABC exporter
Map data
Sample
  • Complex: homodimeric Atm1-type heavy metal transporter
    • Protein or peptide: ATM1-type heavy metal exporter
KeywordsABC transporter / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


Translocases / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATM1-type heavy metal exporter
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria) / Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsFan C / Rees DC
Funding support United States, 1 items
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.
History
DepositionFeb 5, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vqu
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21357.png

Downloads & links

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Map

FileDownload / File: emd_21357.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å		0.83 Å/pix.
x 400 pix.
= 333.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.111826956 - 0.3378546
Average (Standard dev.)0.00039005256 (±0.010648345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8340.8340.834
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z333.600333.600333.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1120.3380.000

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Supplemental data

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Additional map: #1

Fileemd_21357_additional.map
Projections & Slices
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Half map: #2

Fileemd_21357_half_map_1.map
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Histogram

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Half map: #1

Fileemd_21357_half_map_2.map
Projections & Slices
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Sample components

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Entire : homodimeric Atm1-type heavy metal transporter

EntireName: homodimeric Atm1-type heavy metal transporter
Components
  • Complex: homodimeric Atm1-type heavy metal transporter
    • Protein or peptide: ATM1-type heavy metal exporter

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Supramolecule #1: homodimeric Atm1-type heavy metal transporter

SupramoleculeName: homodimeric Atm1-type heavy metal transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Novosphingobium aromaticivorans DSM 12444 (bacteria)
Molecular weightTheoretical: 133 KDa

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Macromolecule #1: ATM1-type heavy metal exporter

MacromoleculeName: ATM1-type heavy metal exporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Molecular weightTheoretical: 67.771602 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPPETATNPK DARHDGWQTL KRFLPYLWPA DNAVLRRRVV GAILMVLLGK ATTLALPFAY KKAVDAMTLG GGAQPALTVA LAFVLAYAL GRFSGVLFDN LRNIVFERVG QDATRHLAEN VFARLHKLSL RFHLARRTGE VTKVIERGTK SIDTMLYFLL F NIAPTVIE ...String:
MPPETATNPK DARHDGWQTL KRFLPYLWPA DNAVLRRRVV GAILMVLLGK ATTLALPFAY KKAVDAMTLG GGAQPALTVA LAFVLAYAL GRFSGVLFDN LRNIVFERVG QDATRHLAEN VFARLHKLSL RFHLARRTGE VTKVIERGTK SIDTMLYFLL F NIAPTVIE LTAVIVIFWL NFGLGLVTAT ILAVIAYVWT TRTITEWRTH LREKMNRLDG QALARAVDSL LNYETVKYFG AE SREEARY ASAARAYADA AVKSENSLGL LNIAQALIVN LLMAGAMAWT VYGWSQGKLT VGDLVFVNTY LTQLFRPLDM LGM VYRTIR QGLIDMAEMF RLIDTHIEVA DVPNAPALVV NRPSVTFDNV VFGYDRDREI LHGLSFEVAA GSRVAIVGPS GAGK STIAR LLFRFYDPWE GRILIDGQDI AHVTQTSLRA ALGIVPQDSV LFNDTIGYNI AYGRDGASRA EVDAAAKGAA IADFI ARLP QGYDTEVGER GLKLSGGEKQ RVAIARTLVK NPPILLFDEA TSALDTRTEQ DILSTMRAVA SHRTTISIAH RLSTIA DSD TILVLDQGRL AEQGSHLDLL RRDGLYAEMW ARQAAESAEV SEAAEHHHHH H

UniProtKB: ATM1-type heavy metal exporter

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
20.0 mMTrisTris
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was reconstituted with MSP1D1 nanodiscs and POPC.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1145444
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mrn

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102076
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

4mrn


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 23
Output model

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

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