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- EMDB-20076: Cryo-EM structure of human TorsinA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-20076
TitleCryo-EM structure of human TorsinA filament
Map dataHuman TorsinA filament
Sample
  • Complex: TorsinA
    • Protein or peptide: Torsin-1A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAAA+ ATPase / nucleotide binding / nuclear envelope / endoplasmic reticulum / membrane / HYDROLASE
Function / homology
Function and homology information


synaptic vesicle membrane organization / nuclear membrane organization / nuclear envelope organization / regulation of dopamine uptake involved in synaptic transmission / protein deneddylation / intermediate filament cytoskeleton organization / regulation of protein localization to cell surface / 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 / protein deneddylation / intermediate filament cytoskeleton organization / 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 / protein localization to nucleus / cytoskeletal protein binding / : / ERAD pathway / cytoplasmic vesicle membrane / secretory granule / 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
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZheng W / Demircioglu FE
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJul 24, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.247
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.247
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oif
  • Surface level: 0.247
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oif
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20076.png

Downloads & links

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Map

FileDownload / File: emd_20076.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman TorsinA filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 192 pix.
= 224.448 Å		1.17 Å/pix.
x 192 pix.
= 224.448 Å		1.17 Å/pix.
x 192 pix.
= 224.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.169 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.247 / Movie #1: 0.247
Minimum - Maximum-0.24623512 - 0.72220606
Average (Standard dev.)0.02794658 (±0.09167829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 224.448 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1691.1691.169
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z224.448224.448224.448
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.2460.7220.028

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Supplemental data

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Sample components

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Entire : TorsinA

EntireName: TorsinA
Components
  • Complex: TorsinA
    • Protein or peptide: Torsin-1A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: TorsinA

SupramoleculeName: TorsinA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Torsin-1A

MacromoleculeName: Torsin-1A / type: protein_or_peptide / ID: 1 / Number of copies: 25 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.590248 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GQKRSLSREA LQKDLDDNLF GQHLAKKIIL NAVFGFINNP KPKKPLTLSL HGWTGTGKNF VSKIIAENIY EGGLNSDYVH LFVATLHFP HASNITLYKD QLQLWIRGNV SACARSIFIF DEMDKMHAGL IDAIKPFLDY YDLVDGVSYQ KAMFIFLSNA G AERITDVA ...String:
GQKRSLSREA LQKDLDDNLF GQHLAKKIIL NAVFGFINNP KPKKPLTLSL HGWTGTGKNF VSKIIAENIY EGGLNSDYVH LFVATLHFP HASNITLYKD QLQLWIRGNV SACARSIFIF DEMDKMHAGL IDAIKPFLDY YDLVDGVSYQ KAMFIFLSNA G AERITDVA LDFWRSGKQR EDIKLKDIEH ALSVSVFNNK NSGFWHSSLI DRNLIDYFVP FLPLEYKHLK MCIRVEMQSR GY EIDEDIV SRVAEEMTFF PKEERVFSDK GCKTVFTKLD YYYDD

UniProtKB: Torsin-1A

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 25 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.53 Å
Applied symmetry - Helical parameters - Δ&Phi: 42.51 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 75909
Segment selectionNumber selected: 75909 / Software - Name: EMAN2 / Software - details: EMAN2 e2helixboxer.py
Startup modelType of model: NONE / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER

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Atomic model buiding 1

Initial modelPDB ID:

5j1s


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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