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- EMDB-21356: Structure of a bacterial Atm1-family ABC exporter with MgADPVO4 bound -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21356 | |||||||||
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Title | Structure of a bacterial Atm1-family ABC exporter with MgADPVO4 bound | |||||||||
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Function / homology | ![]() Translocases / response to mercury ion / ABC-type transporter activity / monoatomic ion transport / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Fan C / Rees DC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 51.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
Images | ![]() | 134.7 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() ![]() | 97.1 MB 95.4 MB 95.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vqtMC ![]() 6pamC ![]() 6panC ![]() 6paoC ![]() 6paqC ![]() 6parC ![]() 6vquC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.8522 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Sharpened map
File | emd_21356_additional.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21356_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_21356_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : homodimeric ATM1-type heavy metal exporter
Entire | Name: homodimeric ATM1-type heavy metal exporter |
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Components |
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-Supramolecule #1: homodimeric ATM1-type heavy metal exporter
Supramolecule | Name: homodimeric ATM1-type heavy metal exporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 133 KDa |
-Macromolecule #1: ATM1-type heavy metal exporter
Macromolecule | Name: ATM1-type heavy metal exporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199 |
Molecular weight | Theoretical: 67.771602 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #3: VANADATE ION
Macromolecule | Name: VANADATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: VO4 |
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Molecular weight | Theoretical: 114.939 Da |
Chemical component information | ![]() ChemComp-VN3: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | The sample was reconstituted with MSP1D1 nanodiscs and POPC. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.6 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 3978816 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic![]() |