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- PDB-5wc0: katanin hexamer in spiral conformation -

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Basic information

Database: PDB / ID: 5wc0
Titlekatanin hexamer in spiral conformation
DescriptorMeiotic spindle formation protein mei-1
KeywordsMOTOR PROTEIN / Microtubule cytoskeleton / microtubule-severing enzyme / AAA ATPase / p60
Specimen sourceCaenorhabditis elegans / animal /
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle)
AuthorsZehr, E.A. / Szyk, A. / Piszczek, G. / Szczesna, E. / Zuo, X. / Roll-Mecak, A.
CitationNat. Struct. Mol. Biol., 2017, 24, 717-725

Nat. Struct. Mol. Biol., 2017, 24, 717-725 Yorodumi Papers
Katanin spiral and ring structures shed light on power stroke for microtubule severing.
Elena Zehr / Agnieszka Szyk / Grzegorz Piszczek / Ewa Szczesna / Xiaobing Zuo / Antonina Roll-Mecak

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 29, 2017 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 23, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Sep 20, 2017Structure modelData collection / Database referencescitation / em_software_citation.journal_volume / _citation.page_first / _citation.page_last / _em_software.name

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Deposited unit
A: Meiotic spindle formation protein mei-1
B: Meiotic spindle formation protein mei-1
C: Meiotic spindle formation protein mei-1
D: Meiotic spindle formation protein mei-1
E: Meiotic spindle formation protein mei-1
F: Meiotic spindle formation protein mei-1
hetero molecules

Theoretical massNumber of molelcules
Total (without water)313,85712

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Polypeptide(L)
Meiotic spindle formation protein mei-1 / Katanin p60 ATPase-containing subunit A1 / Katanin p60 subunit A1 / p60 katanin

Mass: 51802.359 Da / Num. of mol.: 6 / Mutation: E293Q / Source: (gene. exp.) Caenorhabditis elegans / animal / / References: UniProt: P34808, EC:

Cellular component

Molecular function

Biological process

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM

Mass: 507.181 Da / Num. of mol.: 6 / Formula: C10H16N5O13P3

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: katanin / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.31 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenConc.: 0.6 mg/ml / Details: Asembled in 1mM ATP / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 17.5 sec. / Electron dose: 51 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2100
Image scansDimension width: 3838 / Dimension height: 3710 / Movie frames/image: 50


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
Particle selectionNumber of particles selected: 403023
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38072 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322911
ELECTRON MICROSCOPYf_angle_d0.73741372
ELECTRON MICROSCOPYf_dihedral_angle_d9.0419154
ELECTRON MICROSCOPYf_chiral_restr0.0411979
ELECTRON MICROSCOPYf_plane_restr0.0043683

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