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- EMDB-20805: Spastin Hexamer (unsharpened map) -

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Basic information

Entry
Database: EMDB / ID: EMD-20805
TitleSpastin Hexamer (unsharpened map)
Map dataSpastin Hexamer (unsharpened map)
Sample
  • Complex: Spastin Hexamer in complex with substrate peptide
Function / homology
Function and homology information


cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III ...cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane fission / microtubule bundle formation / anterograde axonal transport / mitotic spindle disassembly / protein hexamerization / exit from mitosis / positive regulation of cytokinesis / axonal transport of mitochondrion / beta-tubulin binding / mitotic cytokinesis / alpha-tubulin binding / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / axonogenesis / lipid droplet / isomerase activity / protein homooligomerization / spindle pole / midbody / cytoplasmic vesicle / microtubule binding / nuclear membrane / microtubule / endosome / axon / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Spastin, chordate / Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...Spastin, chordate / Spastin / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHan H / Schubert HL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM112080 United States
CitationJournal: J Biol Chem / Year: 2020
Title: Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation.
Authors: Han Han / Heidi L Schubert / John McCullough / Nicole Monroe / Michael D Purdy / Mark Yeager / Wesley I Sundquist / Christopher P Hill /
Abstract: Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic ...Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic cells by driving the remodeling and severing of microtubules, which are cytoskeletal polymers of tubulin subunits. Here, we demonstrate that a human spastin binds weakly to unmodified peptides from the C-terminal segment of human tubulin α1A/B. A peptide comprising alternating glutamate and tyrosine residues binds more tightly, which is consistent with the known importance of glutamylation for spastin microtubule severing activity. A cryo-EM structure of the spastin-peptide complex at 4.2 Å resolution revealed an asymmetric hexamer in which five spastin subunits adopt a helical, spiral staircase configuration that binds the peptide within the central pore, whereas the sixth subunit of the hexamer is displaced from the peptide/substrate, as if transitioning from one end of the helix to the other. This configuration differs from a recently published structure of spastin from , which forms a six-subunit spiral without a transitioning subunit. Our structure resembles other recently reported AAA unfoldases, including the meiotic clade relative Vps4, and supports a model in which spastin utilizes a hand-over-hand mechanism of tubulin translocation and microtubule remodeling.
History
DepositionOct 4, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseDec 4, 2019-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0182
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0182
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pen
  • Surface level: 0.0182
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20805.png

Downloads & links

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Map

FileDownload / File: emd_20805.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSpastin Hexamer (unsharpened map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0182 / Movie #1: 0.0182
Minimum - Maximum-0.02525849 - 0.07747161
Average (Standard dev.)0.0000002903 (±0.003001832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.336 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0561.0561.056
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z270.336270.336270.336
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ560560560
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0250.0770.000

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Supplemental data

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Sample components

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Entire : Spastin Hexamer in complex with substrate peptide

EntireName: Spastin Hexamer in complex with substrate peptide
Components
  • Complex: Spastin Hexamer in complex with substrate peptide

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Supramolecule #1: Spastin Hexamer in complex with substrate peptide

SupramoleculeName: Spastin Hexamer in complex with substrate peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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