|Entry||Database: EMDB / ID: EMD-20761|
|Title||Katanin hexamer in the spiral conformation in complex with substrate|
|Sample||Hexameric complex of C.elegans katanin bound to polyglutamate peptide:|
Meiotic spindle formation protein mei-1 / Polyglutamate peptide / (ligand) x 2
|Function / homology|
Function and homology information
negative regulation of meiotic spindle elongation / MATH domain binding / katanin complex / meiotic spindle disassembly / meiotic spindle pole / microtubule-severing ATPase / microtubule severing / microtubule-severing ATPase activity / striated muscle myosin thick filament assembly / meiotic spindle organization ...negative regulation of meiotic spindle elongation / MATH domain binding / katanin complex / meiotic spindle disassembly / meiotic spindle pole / microtubule-severing ATPase / microtubule severing / microtubule-severing ATPase activity / striated muscle myosin thick filament assembly / meiotic spindle organization / female meiotic nuclear division / embryo development ending in birth or egg hatching / microtubule depolymerization / meiotic spindle / cytoplasmic microtubule organization / isomerase activity / chromatin / spindle / microtubule binding / microtubule / protein phosphatase binding / ATPase activity / cell division / centrosome / ATP binding / identical protein binding / nucleus / cytoplasm
AAA ATPase, AAA+ lid domain / Katanin p60 subunit A1 / P-loop containing nucleoside triphosphate hydrolase / ATPase, AAA-type, conserved site / AAA+ ATPase domain / ATPase, AAA-type, core
Meiotic spindle formation protein mei-1
|Biological species||Caenorhabditis elegans (roundworm) / synthetic construct (others)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.5 Å|
|Authors||Zehr EA / Roll-Mecak A|
|Funding support|| United States, 1 items |
|Citation||Journal: Dev. Cell / Year: 2020|
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.
|Validation Report||PDB-ID: 6ugd|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_20761.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.08 Å|
|Symmetry||Space group: 1|
CCP4 map header:
+Entire Hexameric complex of C.elegans katanin bound to polyglutamate peptide
|Entire||Name: Hexameric complex of C.elegans katanin bound to polyglutamate peptide|
Number of components: 5
+Component #1: protein, Hexameric complex of C.elegans katanin bound to polyglut...
|Protein||Name: Hexameric complex of C.elegans katanin bound to polyglutamate peptide|
Recombinant expression: No
|Mass||Theoretical: 312 kDa|
|Source||Species: Caenorhabditis elegans (roundworm)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pDEST566 / Strain: BL21(DE3)|
+Component #2: protein, Meiotic spindle formation protein mei-1
|Protein||Name: Meiotic spindle formation protein mei-1 / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 53.576336 kDa|
|Source||Species: Caenorhabditis elegans (roundworm)|
|Source (engineered)||Expression System: Escherichia coli BL21(DE3) (bacteria)|
+Component #3: protein, Polyglutamate peptide
|Protein||Name: Polyglutamate peptide / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 1.825609 kDa|
|Source||Species: synthetic construct (others)|
+Component #4: ligand, ADENOSINE-5'-TRIPHOSPHATE
|Ligand||Name: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 0.507181 kDa|
+Component #5: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/mL / pH: 7.5|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 279.15 K / Humidity: 90 % / Details: Load 5 ul sample, wait 10 sec, blot 4.5 sec.|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 73 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2800.0 nm / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (93.0 - 103.0 K)|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 5911|
-Atomic model buiding
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi