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- PDB-6gzc: heterotetrameric katanin p60:p80 complex -

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Basic information

Entry
Database: PDB / ID: 6gzc
Titleheterotetrameric katanin p60:p80 complex
Components
  • Katanin p60 ATPase-containing subunit A1
  • Katanin p80 WD40 repeat-containing subunit B1
KeywordsHYDROLASE / Katanin / severing enzyme / MICROTUBULE / cytoskeleton
Function / homology
Function and homology information


ATPase regulator activity / katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / positive regulation of microtubule depolymerization / negative regulation of microtubule depolymerization / microtubule bundle formation / microtubule depolymerization ...ATPase regulator activity / katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / positive regulation of microtubule depolymerization / negative regulation of microtubule depolymerization / microtubule bundle formation / microtubule depolymerization / Cul3-RING ubiquitin ligase complex / dynein complex binding / mitotic spindle pole / cytoplasmic microtubule organization / isomerase activity / lipid droplet / neuron migration / protein localization / positive regulation of neuron projection development / spindle pole / spindle / microtubule cytoskeleton / negative regulation of neuron projection development / midbody / growth cone / microtubule binding / microtubule / positive regulation of apoptotic process / cell cycle / protein heterodimerization activity / cell division / axon / centrosome / neuronal cell body / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit, C-terminal / : / : / con80 domain of Katanin / Katanin p60 subunit A1, MIT domain / Katanin p60 subunit A1 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / Vps4 oligomerisation, C-terminal ...Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit, C-terminal / : / : / con80 domain of Katanin / Katanin p60 subunit A1, MIT domain / Katanin p60 subunit A1 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT domain superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Katanin p80 WD40 repeat-containing subunit B1 / Katanin p60 ATPase-containing subunit A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFaltova, L. / Jiang, K. / Frey, D. / Wu, Y. / Capitani, G. / Prota, A.E. / Akhmanova, A. / Steinmetz, M.O. / Kammerer, R.A.
CitationJournal: Structure / Year: 2019
Title: Crystal Structure of a Heterotetrameric Katanin p60:p80 Complex.
Authors: Faltova, L. / Jiang, K. / Frey, D. / Wu, Y. / Capitani, G. / Prota, A.E. / Akhmanova, A. / Steinmetz, M.O. / Kammerer, R.A.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Katanin p80 WD40 repeat-containing subunit B1
B: Katanin p60 ATPase-containing subunit A1
D: Katanin p60 ATPase-containing subunit A1
C: Katanin p80 WD40 repeat-containing subunit B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8208
Polymers65,4844
Non-polymers3364
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-53 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.490, 57.850, 59.770
Angle α, β, γ (deg.)108.32, 101.00, 98.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Katanin p80 WD40 repeat-containing subunit B1 / Katanin p80 subunit B1 / p80 katanin


Mass: 23207.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katnb1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BG40
#2: Protein Katanin p60 ATPase-containing subunit A1 / Katanin p60 subunit A1 / Lipotransin / p60 katanin


Mass: 9534.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katna1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WV86, EC: 3.6.4.3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 10% PEG 8000, 0.1 M HEPES (7.5), 8% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2→43.6 Å / Num. obs: 36685 / % possible obs: 97.9 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Net I/σ(I): 20.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 1.534 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2671 / CC1/2: 0.587 / Rrim(I) all: 1.656 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OW5

5ow5


Resolution: 2→43.575 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.57
RfactorNum. reflection% reflection
Rfree0.2282 1834 5 %
Rwork0.2091 --
obs0.21 36685 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 22 72 3914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043898
X-RAY DIFFRACTIONf_angle_d0.5385248
X-RAY DIFFRACTIONf_dihedral_angle_d9.5032388
X-RAY DIFFRACTIONf_chiral_restr0.038630
X-RAY DIFFRACTIONf_plane_restr0.003641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.41231380.37652622X-RAY DIFFRACTION97
2.0541-2.11450.37341390.33842641X-RAY DIFFRACTION97
2.1145-2.18280.34571410.30162676X-RAY DIFFRACTION97
2.1828-2.26080.29181390.27592658X-RAY DIFFRACTION97
2.2608-2.35130.30251400.25022643X-RAY DIFFRACTION97
2.3513-2.45830.28671410.23242693X-RAY DIFFRACTION98
2.4583-2.58790.28661410.22332672X-RAY DIFFRACTION98
2.5879-2.750.25961430.2212713X-RAY DIFFRACTION98
2.75-2.96230.25031410.22372690X-RAY DIFFRACTION99
2.9623-3.26030.30221430.24092704X-RAY DIFFRACTION99
3.2603-3.73190.2331430.20832722X-RAY DIFFRACTION99
3.7319-4.70090.17821420.17282685X-RAY DIFFRACTION99
4.7009-43.58530.18331430.18552732X-RAY DIFFRACTION99
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)
15.49880.7453-0.9645.0399-1.08577.1381-0.1897-0.1909-0.49930.3202-0.1605-1.02330.02940.8590.44590.37060.03820.05750.80560.00540.8964-193.830944.2192-98.2641
22.08860.55750.82774.5826-0.5291.2098-0.0732-0.0373-0.2286-0.34540.13220.09910.0743-0.1374-0.04320.39170.06020.13070.4074-0.0440.5089-220.171823.7036-92.5951
33.66422.4314-3.25414.5085-3.75218.22930.44861.0298-0.1218-0.73830.0340.0765-0.1212-0.9415-0.30870.87840.18390.09470.7988-0.02490.913-226.280522.2073-102.0665
42.63031.36370.1253.9793-5.34519.2514-0.2303-0.17770.05710.36010.82341.5346-0.0961-1.9149-0.63670.60820.16480.06831.1379-0.03031.0999-236.856421.5617-88.2543
56.00930.8895-0.6065.6747-5.11554.7110.3272-0.49440.39741.78330.57821.2506-0.7772-1.2545-0.89870.86380.04340.26330.53780.03210.8924-222.99260.4423-64.8124
64.89461.0516-1.82535.1585-1.19735.83260.2705-0.6379-0.02891.7515-0.1983-0.084-0.07850.6545-0.18290.864-0.01240.05460.487-0.07070.53-212.28170.3715-61.875
77.76715.0176-4.63653.471-3.25533.61110.30651.29890.2574-0.69340.44850.2656-1.07160.0026-0.68770.7301-0.08130.22680.81330.09310.8648-198.054453.1966-112.8923
83.32362.6483-0.58126.7358-4.85274.26610.35761.4295-0.5281-1.7555-0.0112-1.1205-0.26861.23630.11971.14560.01060.47411.3106-0.05521.0769-191.776448.2121-120.0853
98.04161.0112-3.45336.0663-1.70767.3942-0.49831.102-0.5131-1.40870.0877-1.34590.56081.39320.62320.59240.02280.16831.2182-0.11750.9697-188.483244.3153-111.5526
102.2647-1.1742-0.41884.0386-1.29649.7126-0.04050.10740.1386-0.4959-0.1675-0.27650.84180.59850.39360.36380.10550.06380.4309-0.02770.5876-212.05592.478-78.6296
112.5024-0.6483-0.50146.62790.0932.01350.0491-0.11660.15290.6455-0.01940.1175-0.466-0.0751-0.08530.31340.05820.05390.3716-0.00860.3696-217.938938.658-85.5063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 486 through 536 )
2X-RAY DIFFRACTION2chain 'A' and (resid 537 through 600 )
3X-RAY DIFFRACTION3chain 'A' and (resid 601 through 638 )
4X-RAY DIFFRACTION4chain 'A' and (resid 639 through 658 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 77 )
7X-RAY DIFFRACTION7chain 'D' and (resid 2 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 22 through 45 )
9X-RAY DIFFRACTION9chain 'D' and (resid 46 through 77 )
10X-RAY DIFFRACTION10chain 'C' and (resid 485 through 536 )
11X-RAY DIFFRACTION11chain 'C' and (resid 537 through 656 )

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