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- PDB-5lb7: Complex structure between p60N/p80C katanin and a peptide derived... -

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Basic information

Entry
Database: PDB / ID: 5lb7
TitleComplex structure between p60N/p80C katanin and a peptide derived from ASPM
Components
  • Abnormal spindle-like microcephaly-associated protein homolog
  • Katanin p60 ATPase-containing subunit A1
  • Katanin p80 WD40 repeat-containing subunit B1
KeywordsHYDROLASE / katanin / ASPM / severing enzyme
Function / homology
Function and homology information


negative regulation of asymmetric cell division / forebrain neuroblast division / ATPase regulator activity / katanin complex / spindle localization / microtubule minus-end / meiotic spindle assembly / maintenance of centrosome location / microtubule-severing ATPase / microtubule severing ATPase activity ...negative regulation of asymmetric cell division / forebrain neuroblast division / ATPase regulator activity / katanin complex / spindle localization / microtubule minus-end / meiotic spindle assembly / maintenance of centrosome location / microtubule-severing ATPase / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / positive regulation of microtubule depolymerization / regulation of meiotic cell cycle / neuronal stem cell population maintenance / negative regulation of microtubule depolymerization / microtubule bundle formation / meiotic spindle / microtubule depolymerization / spindle organization / oogenesis / Cul3-RING ubiquitin ligase complex / dynein complex binding / positive regulation of neuroblast proliferation / mitotic spindle pole / negative regulation of neuron differentiation / developmental growth / cytoplasmic microtubule organization / isomerase activity / lipid droplet / neuron migration / brain development / protein localization / cerebral cortex development / positive regulation of neuron projection development / spindle pole / spindle / male gonad development / microtubule cytoskeleton / positive regulation of canonical Wnt signaling pathway / negative regulation of neuron projection development / midbody / growth cone / microtubule binding / spermatogenesis / microtubule / calmodulin binding / apical plasma membrane / 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
Abnormal spindle-like microcephaly-associated protein / Abnormal spindle-like microcephaly-associated protein, ASH domain / Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin / 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 ...Abnormal spindle-like microcephaly-associated protein / Abnormal spindle-like microcephaly-associated protein, ASH domain / Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin / 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 / IQ calmodulin-binding motif / Calponin homology domain / Calponin homology (CH) domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / IQ motif profile. / IQ motif, EF-hand binding site / 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 / Armadillo-type fold / 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 / Immunoglobulin-like fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Katanin p80 WD40 repeat-containing subunit B1 / Abnormal spindle-like microcephaly-associated protein homolog / Katanin p60 ATPase-containing subunit A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsRezabkova, L. / Capitani, G. / Kammerer, R.A. / Steinmetz, M.O.
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
DepositionJun 15, 2016Deposition 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 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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
C: Abnormal spindle-like microcephaly-associated protein homolog


Theoretical massNumber of molelcules
Total (without water)33,8933
Polymers33,8933
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.090, 145.120, 37.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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.: 1
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.: 1
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: Protein/peptide Abnormal spindle-like microcephaly-associated protein homolog / Calmodulin-binding protein Sha1 / Calmodulin-binding protein 1 / Spindle and hydroxyurea checkpoint ...Calmodulin-binding protein Sha1 / Calmodulin-binding protein 1 / Spindle and hydroxyurea checkpoint abnormal protein


Mass: 1007.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CJ27
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 20% PEG 3350, 0.1 M BisTris propane, 0.2 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 45112 / % possible obs: 97.7 % / Redundancy: 24.6 % / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.5→43.868 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2226 903 2 %
Rwork0.1831 --
obs0.1839 45112 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→43.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 0 219 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032030
X-RAY DIFFRACTIONf_angle_d0.5242741
X-RAY DIFFRACTIONf_dihedral_angle_d16.924767
X-RAY DIFFRACTIONf_chiral_restr0.05326
X-RAY DIFFRACTIONf_plane_restr0.003336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4999-1.59390.39191300.31816377X-RAY DIFFRACTION86
1.5939-1.71690.28571530.22267472X-RAY DIFFRACTION100
1.7169-1.88970.26621520.19397463X-RAY DIFFRACTION100
1.8897-2.16320.21111530.14847487X-RAY DIFFRACTION100
2.1632-2.72530.20791550.17387579X-RAY DIFFRACTION100
2.7253-43.88640.21221600.18457831X-RAY DIFFRACTION100

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