+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20327 | |||||||||
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Title | Spastin Hexamer in complex with substrate peptide | |||||||||
Map data | ||||||||||
Sample |
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Keywords | AAA+ ATPase / Microtubule Severing / MOTOR PROTEIN | |||||||||
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 / protein hexamerization / mitotic spindle disassembly / exit from mitosis / axonal transport of mitochondrion / beta-tubulin binding / positive regulation of cytokinesis / mitotic cytokinesis / alpha-tubulin binding / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / lipid droplet / axonogenesis / 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 | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Han H / Schubert HL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20327.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-20327-v30.xml emd-20327.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_20327.png | 72 KB | ||
Filedesc metadata | emd-20327.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20327 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20327 | HTTPS FTP |
-Validation report
Summary document | emd_20327_validation.pdf.gz | 362.2 KB | Display | EMDB validaton report |
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Full document | emd_20327_full_validation.pdf.gz | 361.8 KB | Display | |
Data in XML | emd_20327_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_20327_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20327 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20327 | HTTPS FTP |
-Related structure data
Related structure data | 6pekMC 6penMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10382 (Title: Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. Data size: 1.8 TB Data #1: Unaligned multi-frame movies of ADPBeFx-bound Spastin [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20327.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Spastin Hexamer in complex with substrate peptide
Entire | Name: Spastin Hexamer in complex with substrate peptide |
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Components |
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-Supramolecule #1: Spastin Hexamer in complex with substrate peptide
Supramolecule | Name: Spastin Hexamer in complex with substrate peptide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spastin
Macromolecule | Name: Spastin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: microtubule-severing ATPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.498328 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MAAKRSSGAA PAPASASAPA PVPGGEAERV RVFHKQAFEY ISIALRIDED EKAGQKEQAV EWYKKGIEEL EKGIAVIVTG QGEQCERAR RLQAKMMTNL VMAKDRLQLL ESGAVPKRKD PLTHTSNSLP RSKTVMKTGS AGLSGHHRAP SYSGLSMVSG V KQGSGPAP ...String: MAAKRSSGAA PAPASASAPA PVPGGEAERV RVFHKQAFEY ISIALRIDED EKAGQKEQAV EWYKKGIEEL EKGIAVIVTG QGEQCERAR RLQAKMMTNL VMAKDRLQLL ESGAVPKRKD PLTHTSNSLP RSKTVMKTGS AGLSGHHRAP SYSGLSMVSG V KQGSGPAP TTHKGTPKTN RTNKPSTPTT ATRKKKDLKN FRNVDSNLAN LIMNEIVDNG TAVKFDDIAG QDLAKQALQE IV ILPSLRP ELFTGLRAPA RGLLLFGPPG NGKTMLAKAV AAESNATFFN ISAASLTSKY VGEGEKLVRA LFAVARELQP SII FIDEVD SLLCERREGE HDASRRLKTE FLIEFDGVQS AGDDRVLVMG ATNRPQELDE AVLRRFIKRV YVSLPNEETR LLLL KNLLC KQGSPLTQKE LAQLARMTDG YSGSDLTALA KDAALGPIRE LKPEQVKNMS ASEMRNIRLS DFTESLKKIK RSVSP QTLE AYIRWNKDFG DTTV UniProtKB: Spastin |
-Macromolecule #2: substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU
Macromolecule | Name: substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.479453 KDa |
Sequence | String: EYEYEYEYEY |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119984 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |