+Open data
-Basic information
Entry | Database: PDB / ID: 6oif | |||||||||
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Title | Cryo-EM structure of human TorsinA filament | |||||||||
Components | Torsin-1A | |||||||||
Keywords | HYDROLASE / AAA+ ATPase / nucleotide binding / nuclear envelope / endoplasmic reticulum / membrane | |||||||||
Function / homology | Function and homology information synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / nuclear envelope organization / regulation of dopamine uptake involved in synaptic transmission / intermediate filament cytoskeleton organization / protein deneddylation / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis / misfolded protein binding ...synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / nuclear envelope organization / regulation of dopamine uptake involved in synaptic transmission / intermediate filament cytoskeleton organization / protein deneddylation / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / wound healing, spreading of cells / synaptic vesicle transport / kinesin binding / chaperone cofactor-dependent protein refolding / protein localization to nucleus / ERAD pathway / chaperone-mediated protein folding / cytoskeletal protein binding / secretory granule / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / neuron projection development / unfolded protein binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / nuclear envelope / growth cone / nuclear membrane / response to oxidative stress / cytoskeleton / cell adhesion / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Zheng, W. / Demircioglu, F.E. / Schwartz, T.U. / Egelman, E.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: The AAA + ATPase TorsinA polymerizes into hollow helical tubes with 8.5 subunits per turn. Authors: F Esra Demircioglu / Weili Zheng / Alexander J McQuown / Nolan K Maier / Nicki Watson / Iain M Cheeseman / Vladimir Denic / Edward H Egelman / Thomas U Schwartz / Abstract: TorsinA is an ER-resident AAA + ATPase, whose deletion of glutamate E303 results in the genetic neuromuscular disease primary dystonia. TorsinA is an unusual AAA + ATPase that needs an ...TorsinA is an ER-resident AAA + ATPase, whose deletion of glutamate E303 results in the genetic neuromuscular disease primary dystonia. TorsinA is an unusual AAA + ATPase that needs an external activator. Also, it likely does not thread a peptide substrate through a narrow central channel, in contrast to its closest structural homologs. Here, we examined the oligomerization of TorsinA to get closer to a molecular understanding of its still enigmatic function. We observe TorsinA to form helical filaments, which we analyzed by cryo-electron microscopy using helical reconstruction. The 4.4 Å structure reveals long hollow tubes with a helical periodicity of 8.5 subunits per turn, and an inner channel of ~ 4 nm diameter. We further show that the protein is able to induce tubulation of membranes in vitro, an observation that may reflect an entirely new characteristic of AAA + ATPases. We discuss the implications of these observations for TorsinA function. | |||||||||
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 | 6oif.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6oif.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6oif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oif_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6oif_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 6oif_validation.xml.gz | 184.2 KB | Display | |
Data in CIF | 6oif_validation.cif.gz | 226.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oif ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oif | HTTPS FTP |
-Related structure data
Related structure data | 20076MC 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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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 25 / Rise per n subunits: 5.53 Å / Rotation per n subunits: 42.51 °) |
-Components
#1: Protein | Mass: 32590.248 Da / Num. of mol.: 25 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1A, DQ2, DYT1, TA, TORA / Production host: Escherichia coli (E. coli) References: UniProt: O14656, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | ChemComp-ATP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: TorsinA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | 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: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 42.51 ° / Axial rise/subunit: 5.53 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 75909 | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75909 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5J1S |