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- PDB-5nbt: Apo structure of p60N/p80C katanin -

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Basic information

Entry
Database: PDB / ID: 5nbt
TitleApo structure of p60N/p80C katanin
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 / axon / cell division / centrosome / neuronal cell body / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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
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 / MAD / Resolution: 2.4 Å
AuthorsJiang, K. / Rezabkova, L. / Hua, S. / Liu, Q. / Capitani, G. / Altelaar, A.F.M. / Heck, A.J.R. / Kammerer, R.A. / Steinmetz, M.O. / Akhmanova, A.
CitationJournal: Nat. Cell Biol. / Year: 2017
Title: Microtubule minus-end regulation at spindle poles by an ASPM-katanin complex.
Authors: Jiang, K. / Rezabkova, L. / Hua, S. / Liu, Q. / Capitani, G. / Maarten Altelaar, A.F. / Heck, A.J.R. / Kammerer, R.A. / Steinmetz, M.O. / Akhmanova, A.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Katanin p80 WD40 repeat-containing subunit B1
B: Katanin p60 ATPase-containing subunit A1
C: Katanin p80 WD40 repeat-containing subunit B1
D: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)65,7404
Polymers65,7404
Non-polymers00
Water1,33374
1
A: Katanin p80 WD40 repeat-containing subunit B1
B: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)32,8702
Polymers32,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area11560 Å2
MethodPISA
2
C: Katanin p80 WD40 repeat-containing subunit B1
D: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)32,8702
Polymers32,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-21 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.140, 37.760, 103.090
Angle α, β, γ (deg.)90.00, 93.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23351.980 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: 9518.043 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 27% PEG 3350, 0.1 M BisTris propane (6.0), 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.4→43.262 Å / Num. obs: 22520 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 7 % / Rmerge(I) obs: 1.404 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 4734 / CC1/2: 0.659 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→43.262 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 1126 5.01 %
Rwork0.2445 --
obs0.2469 22494 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 74 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033499
X-RAY DIFFRACTIONf_angle_d0.5824709
X-RAY DIFFRACTIONf_dihedral_angle_d13.8522147
X-RAY DIFFRACTIONf_chiral_restr0.034569
X-RAY DIFFRACTIONf_plane_restr0.003572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.50930.38971390.3252643X-RAY DIFFRACTION99
2.5093-2.64160.36531380.29862609X-RAY DIFFRACTION100
2.6416-2.8070.34311390.29172640X-RAY DIFFRACTION100
2.807-3.02370.35081390.27752651X-RAY DIFFRACTION100
3.0237-3.32790.31791410.26472657X-RAY DIFFRACTION100
3.3279-3.80920.24741400.21922677X-RAY DIFFRACTION100
3.8092-4.79820.241420.20342698X-RAY DIFFRACTION100
4.7982-43.26890.311480.2472793X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 68.5247 Å / Origin y: 16.3926 Å / Origin z: 25.4615 Å
111213212223313233
T0.3813 Å2-0.0022 Å2-0.0049 Å2-0.251 Å20.0417 Å2--0.3225 Å2
L0.9433 °2-0.049 °20.0982 °2-0.6171 °20.3845 °2--1.8788 °2
S-0.0096 Å °0.0179 Å °0.0415 Å °-0.0123 Å °0.1079 Å °-0.0056 Å °0.0225 Å °0.0876 Å °-0.1181 Å °
Refinement TLS groupSelection details: all

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