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Yorodumi- PDB-7n59: Structure of AtAtm3 in the inward-facing conformation with GSSG bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n59 | ||||||
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Title | Structure of AtAtm3 in the inward-facing conformation with GSSG bound | ||||||
Components | ABC transporter B family member 25, mitochondrial | ||||||
Keywords | MEMBRANE PROTEIN / ATPase | ||||||
Function / homology | Function and homology information regulation of chlorophyll biosynthetic process / chloroplast organization / pollen development / root development / regulation of catalytic activity / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / ABC-type transporter activity / chromosome organization ...regulation of chlorophyll biosynthetic process / chloroplast organization / pollen development / root development / regulation of catalytic activity / Mo-molybdopterin cofactor biosynthetic process / chloroplast envelope / plastid / ABC-type transporter activity / chromosome organization / response to cadmium ion / chloroplast / response to lead ion / iron ion transport / intracellular iron ion homeostasis / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Fan, C. / Rees, D.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2022 Title: Glutathione binding to the plant Atm3 transporter and implications for the conformational coupling of ABC transporters. Authors: Chengcheng Fan / Douglas C Rees / Abstract: The ATP binding cassette (ABC) transporter of mitochondria (Atm) from (Atm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by ...The ATP binding cassette (ABC) transporter of mitochondria (Atm) from (Atm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by exporting glutathione derivatives. Using single-particle cryo-electron microscopy, we have determined four structures of Atm3 in three different conformational states: two inward-facing conformations (with and without bound oxidized glutathione [GSSG]), together with closed and outward-facing states stabilized by MgADP-VO. These structures not only provide a structural framework for defining the alternating access transport cycle, but also reveal the paucity of cysteine residues in the glutathione binding site that could potentially form inhibitory mixed disulfides with GSSG. Despite extensive efforts, we were unable to prepare the ternary complex of Atm3 containing both GSSG and MgATP. A survey of structurally characterized type IV ABC transporters that includes Atm3 establishes that while nucleotides are found associated with all conformational states, they are effectively required to stabilize occluded, closed, and outward-facing conformations. In contrast, transport substrates have only been observed associated with inward-facing conformations. The absence of structures with dimerized nucleotide binding domains containing both nucleotide and transport substrate suggests that this form of the ternary complex exists only transiently during the transport cycle. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n59.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n59.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 7n59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n59_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7n59_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7n59_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 7n59_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/7n59 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/7n59 | HTTPS FTP |
-Related structure data
Related structure data | 24183MC 7n58C 7n5aC 7n5bC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 81793.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCB25, ATM3, STA1, At5g58270, MCK7.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LVM1 #2: Chemical | ChemComp-GDS / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: AtAtm3 in detergent / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.14 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.7 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6426 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2510131 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 259020 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 84 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6PAM Pdb chain-ID: A / Accession code: 6PAM / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.27 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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