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Yorodumi- PDB-7pro: Structure of CtAtm1 in the inward-open with Glutathione-complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pro | ||||||||||||
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Title | Structure of CtAtm1 in the inward-open with Glutathione-complexed [2Fe-2S] cluster bound | ||||||||||||
Components | Putative iron-sulfur protein | ||||||||||||
Keywords | MEMBRANE PROTEIN / ABC exporter | ||||||||||||
Function / homology | Function and homology information ABC-type transporter activity / iron ion transport / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||
Authors | Li, P. / Wang, K.T. / Gourdon, P.E. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria. Authors: Ping Li / Amber L Hendricks / Yong Wang / Rhiza Lyne E Villones / Karin Lindkvist-Petersson / Gabriele Meloni / J A Cowan / Kaituo Wang / Pontus Gourdon / Abstract: In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest ...In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 Å, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pro.cif.gz | 206.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pro.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 7pro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/7pro ftp://data.pdbj.org/pub/pdb/validation_reports/pr/7pro | HTTPS FTP |
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-Related structure data
Related structure data | 13609MC 7pqxC 7pr1C 7pruC 7psdC C: citing same article (ref.) M: map data used to model this data |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999995699517, -0.000574685335277, -0.00287587989477), (0.000574718830765, -0.999999834791, -1.08206406662E-5), (-0.00287587320118, -1.24734164627E-5, 0.99999586459) ...NCS oper: (Code: given Matrix: (-0.999995699517, -0.000574685335277, -0.00287587989477), Vector: |
-Components
#1: Protein | Mass: 77199.812 Da / Num. of mol.: 2 / Mutation: E603Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0050000 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SBE6 |
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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: atm1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81145 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7PQX | ||||||||||||||||||||||||
Refinement | Highest resolution: 3 Å / Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.49 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.000706761069282 Å |