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- PDB-6oif: Cryo-EM structure of human TorsinA filament -

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Basic information

Entry
Database: PDB / ID: 6oif
TitleCryo-EM structure of human TorsinA filament
ComponentsTorsin-1A
KeywordsHYDROLASE / AAA+ ATPase / nucleotide binding / nuclear envelope / endoplasmic reticulum / membrane
Function / homology
Function and homology information


synaptic vesicle membrane organization / nuclear membrane organization / nuclear envelope organization / regulation of dopamine uptake involved in synaptic transmission / regulation of protein localization to cell surface / intermediate filament cytoskeleton organization / protein deneddylation / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / wound healing, spreading of cells ...synaptic vesicle membrane organization / nuclear membrane organization / nuclear envelope organization / regulation of dopamine uptake involved in synaptic transmission / regulation of protein localization to cell surface / intermediate filament cytoskeleton organization / protein deneddylation / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / wound healing, spreading of cells / synaptic vesicle transport / : / kinesin binding / protein localization to nucleus / cytoskeletal protein binding / : / ERAD pathway / secretory granule / cytoplasmic vesicle membrane / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuron projection development / synaptic vesicle / unfolded protein binding / nuclear envelope / Cargo recognition for clathrin-mediated endocytosis / growth cone / response to oxidative stress / nuclear membrane / 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
Torsin / Torsin 1/2 / : / Torsin / Torsin-1A, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Torsin-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZheng, W. / Demircioglu, F.E. / Schwartz, T.U. / Egelman, E.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR065484 United States
CitationJournal: 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
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Torsin-1A
B: Torsin-1A
C: Torsin-1A
D: Torsin-1A
E: Torsin-1A
F: Torsin-1A
G: Torsin-1A
H: Torsin-1A
I: Torsin-1A
J: Torsin-1A
K: Torsin-1A
L: Torsin-1A
M: Torsin-1A
N: Torsin-1A
O: Torsin-1A
P: Torsin-1A
Q: Torsin-1A
R: Torsin-1A
S: Torsin-1A
T: Torsin-1A
U: Torsin-1A
V: Torsin-1A
W: Torsin-1A
X: Torsin-1A
Y: Torsin-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)827,43650
Polymers814,75625
Non-polymers12,68025
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical 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 °)

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Components

#1: Protein ...
Torsin-1A / Dystonia 1 protein / Torsin ATPase-1A / Torsin family 1 member A


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 / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: TorsinA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionEMAN2 e2helixboxer.py
4CTFFIND3CTF correction
5SPIDERCTF correction
8RosettaEMmodel fitting
10SPIDERinitial Euler assignment
11SPIDERfinal Euler assignment
13SPIDER3D reconstruction
14Cootmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 42.51 ° / Axial rise/subunit: 5.53 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 75909
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75909 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 5J1S

5j1s


Accession code: 5J1S / Source name: PDB / Type: experimental model

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