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- EMDB-20763: Katanin hexamer in the ring conformation with resolved protomer o... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20763 | |||||||||
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Title | Katanin hexamer in the ring conformation with resolved protomer one in complex with substrate | |||||||||
![]() | Katanin hexamer in the ring conformation with resolved P1 in complex with substrate | |||||||||
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![]() | katanin / microtubule-severing / MEI-1 / microtubule cytoskeleton / MOTOR PROTEIN | |||||||||
Function / homology | ![]() negative regulation of meiotic spindle elongation / MATH domain binding / striated muscle myosin thick filament assembly / katanin complex / meiotic spindle disassembly / meiotic spindle pole / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / female meiotic nuclear division ...negative regulation of meiotic spindle elongation / MATH domain binding / striated muscle myosin thick filament assembly / katanin complex / meiotic spindle disassembly / meiotic spindle pole / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / female meiotic nuclear division / meiotic spindle organization / meiotic spindle / embryo development ending in birth or egg hatching / microtubule depolymerization / isomerase activity / spindle pole / spindle / microtubule cytoskeleton / protein phosphatase binding / microtubule binding / microtubule / molecular adaptor activity / cell division / centrosome / chromatin / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Zehr EA / Roll-Mecak A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Katanin Grips the β-Tubulin Tail through an Electropositive Double Spiral to Sever Microtubules. Authors: Elena A Zehr / Agnieszka Szyk / Ewa Szczesna / Antonina Roll-Mecak / ![]() Abstract: The AAA ATPase katanin severs microtubules. It is critical in cell division, centriole biogenesis, and neuronal morphogenesis. Its mutation causes microcephaly. The microtubule templates katanin ...The AAA ATPase katanin severs microtubules. It is critical in cell division, centriole biogenesis, and neuronal morphogenesis. Its mutation causes microcephaly. The microtubule templates katanin hexamerization and activates its ATPase. The structural basis for these activities and how they lead to severing is unknown. Here, we show that β-tubulin tails are necessary and sufficient for severing. Cryoelectron microscopy (cryo-EM) structures reveal the essential tubulin tail glutamates gripped by a double spiral of electropositive loops lining the katanin central pore. Each spiral couples allosterically to the ATPase and binds alternating, successive substrate residues, with consecutive residues coordinated by adjacent protomers. This tightly couples tail binding, hexamerization, and ATPase activation. Hexamer structures in different states suggest an ATPase-driven, ratchet-like translocation of the tubulin tail through the pore. A disordered region outside the AAA core anchors katanin to the microtubule while the AAA motor exerts the forces that extract tubulin dimers and sever the microtubule. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 38.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 192.9 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 543.8 KB | Display | ![]() |
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Full document | ![]() | 543.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ugfMC ![]() 6ugdC ![]() 6ugeC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Katanin hexamer in the ring conformation with resolved P1 in complex with substrate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Hexameric complex of C.elegans katanin bound to polyglutamate peptide
Entire | Name: Hexameric complex of C.elegans katanin bound to polyglutamate peptide |
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Components |
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-Supramolecule #1: Hexameric complex of C.elegans katanin bound to polyglutamate peptide
Supramolecule | Name: Hexameric complex of C.elegans katanin bound to polyglutamate peptide type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 312 KDa |
-Macromolecule #1: Meiotic spindle formation protein mei-1
Macromolecule | Name: Meiotic spindle formation protein mei-1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: microtubule-severing ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.576336 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSFTMASMTG GQQMGRGSMN GDVQSVIRGY LERAQVAKTM SDAGRWNEAG DLLRQLMTDV KSCKISASNR DEHDARNTFL RALEANLKL VQQNVRDEDD LHEAMTRQSG SPEPPADPDV WSKPSPPLPS SSKFGATKKG VGAAGPRPRE ISKSTSSMST N PADVKPAN ...String: GSFTMASMTG GQQMGRGSMN GDVQSVIRGY LERAQVAKTM SDAGRWNEAG DLLRQLMTDV KSCKISASNR DEHDARNTFL RALEANLKL VQQNVRDEDD LHEAMTRQSG SPEPPADPDV WSKPSPPLPS SSKFGATKKG VGAAGPRPRE ISKSTSSMST N PADVKPAN PTQGILPQNS AGDSFDASAY DAYIVQAVRG TMATNTENTM SLDDIIGMHD VKQVLHEAVT LPLLVPEFFQ GL RSPWKAM VLAGPPGTGK TLIARAIASE SSSTFFTVSS TDLSSKWRGD SEKIVRLLFE LARFYAPSII FIDQIDTLGG QRG NSGEHE ASRRVKSEFL VQMDGSQNKF DSRRVFVLAA TNIPWELDEA LRRRFEKRIF IPLPDIDARK KLIEKSMEGT PKSD EINYD DLAARTEGFS GADVVSLCRT AAINVLRRYD TKSLRGGELT AAMESLKAEL VRNIDFEAAL QAVSPSAGPD TMLKC KEWC DSFGAM UniProtKB: Meiotic spindle formation protein mei-1 |
-Macromolecule #2: Polyglutamate peptide
Macromolecule | Name: Polyglutamate peptide / 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: 1.567381 KDa |
Sequence | String: EEEEEEEEEE EE |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279.15 K / Instrument: LEICA EM GP / Details: Load 5 ul sample, wait 10 sec, blot 4.5 sec. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 93.0 K / Max: 103.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 4 / Number real images: 5911 / Average exposure time: 10.0 sec. / Average electron dose: 73.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
Output model | ![]() PDB-6ugf: |