+Open data
-Basic information
Entry | Database: PDB / ID: 6pdw | ||||||||||||
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Title | Msp1-substrate complex in closed conformation | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / membrane protein / tail-anchored protein / protein quality control | ||||||||||||
Function / homology | Function and homology information extraction of mislocalized protein from mitochondrial outer membrane / mitochondrial outer membrane / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Wang, L. / Myasnikov, A. / Pan, X. / Walter, P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2020 Title: Structure of the AAA protein Msp1 reveals mechanism of mislocalized membrane protein extraction. Authors: Lan Wang / Alexander Myasnikov / Xingjie Pan / Peter Walter / Abstract: The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly ...The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly engages them during the energetically unfavorable extraction process remains a mystery. To address this question, we solved cryo-EM structures of Msp1-substrate complexes at near-atomic resolution. Akin to other AAA proteins, Msp1 forms hexameric spirals that translocate substrates through a central pore. A singular hydrophobic substrate recruitment site is exposed at the spiral's seam, which we propose positions the substrate for entry into the pore. There, a tight web of aromatic amino acids grips the substrate in a sequence-promiscuous, hydrophobic milieu. Elements at the intersubunit interfaces coordinate ATP hydrolysis with the subunits' positions in the spiral. We present a comprehensive model of Msp1's mechanism, which follows general architectural principles established for other AAA proteins yet specializes Msp1 for its unique role in membrane protein extraction. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pdw.cif.gz | 265.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pdw.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pdw_validation.pdf.gz | 966.4 KB | Display | wwPDB validaton report |
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Full document | 6pdw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6pdw_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 6pdw_validation.cif.gz | 79.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/6pdw ftp://data.pdbj.org/pub/pdb/validation_reports/pd/6pdw | HTTPS FTP |
-Related structure data
Related structure data | 20318MC 6pdyC 6pe0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42599.152 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0034230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S654 #2: Protein/peptide | | Mass: 869.063 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-ADP / #4: Chemical | #5: Chemical | ChemComp-MG / |
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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: Msp1-substrate complex in closed conformation / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.24 MDa / Experimental value: YES |
Source (natural) | Organism: Chaetomium thermophilum (fungus) |
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 |
Specimen support | Details: unspecified |
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 |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48861 / Symmetry type: POINT |