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- PDB-6b5d: Structural Basis for Katanin Self-Assembly -

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Basic information

Entry
Database: PDB / ID: 6b5d
TitleStructural Basis for Katanin Self-Assembly
ComponentsMeiotic spindle formation protein mei-1
KeywordsCELL CYCLE / Katanin / AAA ATPase / Microtubule severing protein / Meiotic spindle formation protein mei-1
Function / homology
Function and homology information


negative regulation of meiotic spindle elongation / MATH domain binding / striated muscle myosin thick filament assembly / meiotic spindle disassembly / katanin complex / 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 / meiotic spindle disassembly / katanin complex / 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 ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Meiotic spindle formation protein mei-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsNithianantham, S. / Al-Bassam, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110283 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for disassembly of katanin heterododecamers.
Authors: Nithianantham, S. / McNally, F.J. / Al-Bassam, J.
History
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,0952
Polymers34,6681
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.830, 98.830, 75.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 34667.941 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) / Strain (production host): BL21(DE3) / References: UniProt: P34808, EC: 3.6.4.3
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY
Sequence detailsKatanin is a microtubule-severing protein. It is composed of a AAA ATPase subunit and a regulatory ...Katanin is a microtubule-severing protein. It is composed of a AAA ATPase subunit and a regulatory subunit (Mei-1/2). Katanin crystals only contained an AAA ATPase domain. Authors indicate: we observed degradation during crystallization likely due to sensitivity to proteolysis at the AAA-MIT linker region.

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 and 0.7 M Sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 28, 2017
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→85.589 Å / Num. all: 7653 / Num. obs: 7653 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 85.7 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.112 / Rsym value: 0.076 / Net I/av σ(I): 8.9 / Net I/σ(I): 13 / Num. measured all: 37571
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.2750.6241.2559211180.3410.7780.6242.4100
3.27-3.474.30.41.8450210360.2370.5130.43.499.5
3.47-3.715.20.2073.550189730.1140.2640.2076.499.8
3.71-45.20.1325.549099410.0720.1690.1329.899.7
4-4.384.90.088.841978550.0460.1050.0814.8100
4.38-4.94.70.05412.736077630.0340.0770.05418.899.5
4.9-5.665.30.05811.736476900.0370.0870.05819.6100
5.66-6.934.50.0689.525495660.0480.1050.06818.798
6.93-9.85.20.02920.923584540.0250.0580.02934.7100
9.8-56.4424.60.01831.711922570.0250.0540.01841.197.7

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.1→56.442 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 382 5 %Random selection
Rwork0.2083 7253 --
obs0.2106 7635 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.24 Å2 / Biso mean: 99.2003 Å2 / Biso min: 39.38 Å2
Refinement stepCycle: final / Resolution: 3.1→56.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 27 0 2229
Biso mean--86.36 --
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032264
X-RAY DIFFRACTIONf_angle_d0.7293063
X-RAY DIFFRACTIONf_chiral_restr0.055358
X-RAY DIFFRACTIONf_plane_restr0.004388
X-RAY DIFFRACTIONf_dihedral_angle_d14.1251387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.54860.34811270.258223992526100
3.5486-4.47050.27161210.206724212542100
4.4705-56.45090.22021340.19492433256799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.10780.44560.13840.5971-0.41720.85770.23350.1711-0.28120.04-0.0911-0.36020.05390.11730.0120.45860.0189-0.08210.5323-0.03630.562894.116731.3932-1.8456
20.6972-0.3389-0.56120.2580.3080.5916-0.0107-0.26040.2796-0.1009-0.23690.22060.1355-0.185-0.00030.5949-0.04560.05770.61710.0040.592359.443733.10710.9823
30.0030.00010.0030.0438-0.02340.01450.0468-0.0792-0.00780.14610.22280.1515-0.2676-0.008800.68560.0098-0.20710.9721-0.00190.873980.817228.342316.3421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 360)A164 - 360
2X-RAY DIFFRACTION2chain 'A' and (resid 361 through 447 )A361 - 447
3X-RAY DIFFRACTION3chain 'A' and (resid 448 through 468 )A448 - 468

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