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- PDB-5wc1: katanin AAA ATPase domain -

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Basic information

Entry
Database: PDB / ID: 5wc1
Titlekatanin AAA ATPase domain
ComponentsMeiotic spindle formation protein mei-1
KeywordsCYTOSOLIC PROTEIN / microtubule severing enzyme
Function / homology
Function and homology information


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 / microtubule binding / protein phosphatase binding / microtubule / molecular adaptor activity / cell division / centrosome / chromatin / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Katanin p60 subunit A1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain ...Katanin p60 subunit A1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Meiotic spindle formation protein mei-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSzyk, A. / Roll-Mecak, A.
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Katanin spiral and ring structures shed light on power stroke for microtubule severing.
Authors: Elena Zehr / Agnieszka Szyk / Grzegorz Piszczek / Ewa Szczesna / Xiaobing Zuo / Antonina Roll-Mecak /
Abstract: Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases important for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack ...Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases important for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of known 3D structures for these enzymes, their mechanism of action has remained poorly understood. Here we report the X-ray crystal structure of the monomeric AAA katanin module from Caenorhabditis elegans and cryo-EM reconstructions of the hexamer in two conformations. The structures reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to microtubule-severing enzymes and critical for their function. The reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes interprotomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiotic spindle formation protein mei-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9943
Polymers51,8021
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.363, 99.363, 76.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mei-1, T01G9.5 / Production host: Escherichia coli (E. coli) / References: UniProt: P34808, EC: 3.6.4.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 297 K / Method: vapor diffusion / Details: 1.0 M ammonium sulfate 0.1 M Tris pH 7.8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 7090 / % possible obs: 98.7 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 36

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9P

3b9p


Resolution: 3.3→49.682 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3075 648 10.04 %
Rwork0.2475 --
obs0.2535 6451 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 10 0 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031820
X-RAY DIFFRACTIONf_angle_d0.5732486
X-RAY DIFFRACTIONf_dihedral_angle_d11.6711091
X-RAY DIFFRACTIONf_chiral_restr0.039312
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.55480.3781330.25571150X-RAY DIFFRACTION100
3.5548-3.91240.31961290.23181176X-RAY DIFFRACTION100
3.9124-4.47830.27291330.20961175X-RAY DIFFRACTION100
4.4783-5.64090.28991320.25261158X-RAY DIFFRACTION99
5.6409-49.68710.31871210.26651144X-RAY DIFFRACTION94

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