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Yorodumi- PDB-7upt: Human mitochondrial AAA protein ATAD1 (with a catalytic dead muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7upt | ||||||||||||
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Title | Human mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (open conformation) | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / AAA protein / mitochondria / tail-anchored protein / membrane protein | ||||||||||||
Function / homology | Function and homology information extraction of mislocalized protein from mitochondrial outer membrane / membrane protein dislocase activity / Class I peroxisomal membrane protein import / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / negative regulation of synaptic transmission, glutamatergic / regulation of postsynaptic neurotransmitter receptor internalization / peroxisomal membrane / positive regulation of receptor internalization / learning / memory ...extraction of mislocalized protein from mitochondrial outer membrane / membrane protein dislocase activity / Class I peroxisomal membrane protein import / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / negative regulation of synaptic transmission, glutamatergic / regulation of postsynaptic neurotransmitter receptor internalization / peroxisomal membrane / positive regulation of receptor internalization / learning / memory / postsynaptic membrane / mitochondrial outer membrane / glutamatergic synapse / ATP hydrolysis activity / ATP binding / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Wang, L. / Toutkoushian, H. / Belyy, V. / Kokontis, C. / Walter, P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2022 Title: Conserved structural elements specialize ATAD1 as a membrane protein extraction machine. Authors: Lan Wang / Hannah Toutkoushian / Vladislav Belyy / Claire Y Kokontis / Peter Walter / Abstract: The mitochondrial AAA (TPase ssociated with diverse cellular ctivities) protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the ...The mitochondrial AAA (TPase ssociated with diverse cellular ctivities) protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondria's protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1's mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. Among these features in Msp1 was the utilization of multiple aromatic amino acids to firmly grip the substrate in the central pore. However, it was not clear whether the aromatic nature of these amino acids were required, or if they could be functionally replaced by aliphatic amino acids. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. We developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1's activity in live cells and showed that both aromatic amino acids in pore-loop 1 are required for ATAD1's function and cannot be substituted by aliphatic amino acids. A short α-helix at the C-terminus strongly facilitates ATAD1's oligomerization, a structural feature that distinguishes ATAD1 from its closely related proteins. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7upt.cif.gz | 308.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7upt.ent.gz | 249 KB | Display | PDB format |
PDBx/mmJSON format | 7upt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/7upt ftp://data.pdbj.org/pub/pdb/validation_reports/up/7upt | HTTPS FTP |
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-Related structure data
Related structure data | 26675MC 7uprC 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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-Components
#1: Protein | Mass: 38289.855 Da / Num. of mol.: 6 / Mutation: E193Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD1, FNP001 / Production host: Escherichia coli (E. coli) References: UniProt: Q8NBU5, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate #2: Protein/peptide | | Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ATP / 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: ATAD1-substrate complex in open conformation / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.2 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21DE3 | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Specimen | Conc.: 4 mg/ml / 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: SPOT SCAN |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45003 / Symmetry type: POINT |