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- PDB-6pek: Structure of Spastin Hexamer (Subunit A-E) in complex with substr... -

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Basic information

Entry
Database: PDB / ID: 6pek
TitleStructure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide
Components
  • Spastin
  • substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU
KeywordsMOTOR PROTEIN / AAA+ ATPase / Microtubule Severing
Function / homology
Function and homology information


membrane fission / cytokinetic process / nuclear envelope reassembly / positive regulation of microtubule depolymerization / microtubule severing / microtubule-severing ATPase / microtubule-severing ATPase activity / cytoskeleton-dependent cytokinesis / endoplasmic reticulum tubular network / mitotic spindle disassembly ...membrane fission / cytokinetic process / nuclear envelope reassembly / positive regulation of microtubule depolymerization / microtubule severing / microtubule-severing ATPase / microtubule-severing ATPase activity / cytoskeleton-dependent cytokinesis / endoplasmic reticulum tubular network / mitotic spindle disassembly / exit from mitosis / axonal transport of mitochondrion / anterograde axonal transport / microtubule bundle formation / positive regulation of cytokinesis / protein hexamerization / beta-tubulin binding / alpha-tubulin binding / cytoplasmic microtubule organization / metabolic process / lipid droplet / axon cytoplasm / mitotic cytokinesis / isomerase activity / axonogenesis / spindle / midbody / endoplasmic reticulum to Golgi vesicle-mediated transport / protein homooligomerization / cytoplasmic vesicle / microtubule / microtubule binding / nuclear membrane / endosome / ATPase activity / protein-containing complex binding / centrosome / endoplasmic reticulum membrane / perinuclear region of cytoplasm / extracellular exosome / integral component of membrane / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
AAA ATPase, AAA+ lid domain / Spastin, chordate / P-loop containing nucleoside triphosphate hydrolase / Spastin / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain
Spastin
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHan, H. / Schubert, H.L. / McCullough, J. / Monroe, N. / Sundquist, W.I. / Hill, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM112080 United States
CitationJournal: J. Biol. Chem. / Year: 2019
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 a1A/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, while 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 Drosophila melanogaster, 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Spastin
B: Spastin
C: Spastin
D: Spastin
E: Spastin
G: substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,46819
Polymers273,9716
Non-polymers2,49713
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Spastin / / Spastic paraplegia 4 protein


Mass: 54498.328 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAST, ADPSP, FSP2, KIAA1083, SPG4 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q9UBP0, microtubule-severing ATPase
#2: Protein/peptide substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU


Mass: 1479.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Magnesium
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spastin Hexamer in complex with substrate peptide / Type: COMPLEX / Entity ID: 1,2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 57 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119984 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00122510
f_angle_d0.4640835
f_dihedral_angle_d3.0298868
f_chiral_restr0.0331753
f_plane_restr0.0013299

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