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Yorodumi- PDB-8c0v: Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c0v | |||||||||||||||
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Title | Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate in single seam state | |||||||||||||||
Components |
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Keywords | TRANSLOCASE / AAA ATPase / peroxisomes / peroxisome biogenesis / peroxisome biogenesis disorders / Zellweger Syndrome | |||||||||||||||
Function / homology | Function and homology information protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein transporter activity / peroxisomal membrane / ATPase complex / protein unfolding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / peroxisome / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Ruettermann, M. / Koci, M. / Lill, P. / Geladas, E.D. / Kaschani, F. / Klink, B.U. / Erdmann, R. / Gatsogiannis, C. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Authors: Maximilian Rüttermann / Michelle Koci / Pascal Lill / Ermis Dionysios Geladas / Farnusch Kaschani / Björn Udo Klink / Ralf Erdmann / Christos Gatsogiannis / Abstract: The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental ...The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c0v.cif.gz | 953.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c0v.ent.gz | 775.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c0v_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8c0v_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8c0v_validation.xml.gz | 148.6 KB | Display | |
Data in CIF | 8c0v_validation.cif.gz | 223.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/8c0v ftp://data.pdbj.org/pub/pdb/validation_reports/c0/8c0v | HTTPS FTP |
-Related structure data
Related structure data | 16372MC 8c0wC 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
-Peroxisomal ATPase ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 92758.891 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PEX1, PAS1, YKL197C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): MH272-3f/alpha References: UniProt: P24004, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Protein | Mass: 115687.094 Da / Num. of mol.: 3 / Mutation: E832Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PEX6, PAS8, YNL329C, N0310 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): MH272-3f/alpha References: UniProt: P33760, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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-Protein/peptide , 1 types, 1 molecules R
#3: Protein/peptide | Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: MH272-3f/alpha |
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-Non-polymers , 3 types, 22 molecules
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / #6: Chemical | |
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-Details
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 |
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Molecular weight | Value: 0.774 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: MH272-3f/alpha / Plasmid: pESC-URA Vector | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE Details: Grids were blotted for 3.5 sec and plunge-frozen after 1 sec drain time at 100% humidity |
-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: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 16763 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1259079 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164610 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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