+Open data
-Basic information
Entry | Database: PDB / ID: 7pqx | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of CtAtm1 in the inward-facing open conformation | ||||||||||||
Components | Putative iron-sulfur protein | ||||||||||||
Keywords | MEMBRANE PROTEIN / ABC exporter | ||||||||||||
Function / homology | Function and homology information ABC-type transporter activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||||||||
Authors | Li, P. / Wang, K.T. / Gourdon, P.E. | ||||||||||||
Funding support | Denmark, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pqx.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pqx.ent.gz | 164.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pqx_validation.pdf.gz | 833 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7pqx_full_validation.pdf.gz | 838.1 KB | Display | |
Data in XML | 7pqx_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 7pqx_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pqx ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pqx | HTTPS FTP |
-Related structure data
Related structure data | 13606MC 7pr1C 7proC 7pruC 7psdC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999999997251, 1.30178208235E-5, -7.29919666903E-5), (-1.30212808778E-5, -0.999999998792, 4.74029451335E-5), (-7.29913495191E-5, 4.74038954521E-5, 0.999999996213) ...NCS oper: (Code: given Matrix: (-0.999999997251, 1.30178208235E-5, -7.29919666903E-5), Vector: |
-Components
#1: Protein | Mass: 77200.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0050000 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SBE6 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: atm1 dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (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 |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 defocus max: 2600 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120619 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 4MYC Accession code: 4MYC / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.41 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.000708094711063 Å |