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- PDB-2rpa: The solution structure of N-terminal domain of microtubule severi... -

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Basic information

Entry
Database: PDB / ID: 2rpa
TitleThe solution structure of N-terminal domain of microtubule severing enzyme
ComponentsKatanin p60 ATPase-containing subunit A1
KeywordsHYDROLASE / AAA ATPase / ATP-binding / Cell cycle / Cell division / Cytoplasm / Microtubule / microtubule severing enzyme / Mitosis / Nucleotide-binding
Function / homology
Function and homology information


katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / microtubule bundle formation / Cul3-RING ubiquitin ligase complex / dynein complex binding / mitotic spindle pole / cytoplasmic microtubule organization / isomerase activity ...katanin complex / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / microtubule bundle formation / Cul3-RING ubiquitin ligase complex / dynein complex binding / mitotic spindle pole / cytoplasmic microtubule organization / isomerase activity / lipid droplet / neuron migration / protein localization / spindle pole / spindle / microtubule cytoskeleton / negative regulation of neuron projection development / midbody / growth cone / microtubule binding / microtubule / cell cycle / protein heterodimerization activity / axon / cell division / centrosome / neuronal cell body / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / : / 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 ...: / : / 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 / 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 p60 ATPase-containing subunit A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, rigid body restrained molecular dynamics, dihedral angle molecular dynamics
AuthorsIwaya, N. / Kuwahara, Y. / Unzai, S. / Nagata, T. / Tomii, K. / Goda, N. / Tochio, H. / Shirakawa, M. / Hiroaki, H.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A common substrate recognition mode conserved between katanin P60 and VPS4 governs microtubule severing and membrane skeleton reorganization
Authors: Iwaya, N. / Kuwahara, Y. / Fujiwara, Y. / Goda, N. / Tenno, T. / Akiyama, K. / Mase, S. / Tochio, H. / Ikegami, T. / Shirakawa, M. / Hiroaki, H.
History
DepositionMay 13, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Katanin p60 ATPase-containing subunit A1


Theoretical massNumber of molelcules
Total (without water)9,2571
Polymers9,2571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Katanin p60 ATPase-containing subunit A1 / Katanin p60 subunit A1 / p60 katanin / Lipotransin


Mass: 9256.642 Da / Num. of mol.: 1 / Fragment: N-teminal domain, residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Katna1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WV86, EC: 3.6.4.3
Sequence detailsTHE NUMBERING OF THE PROTEIN SIMPLY SKIPS NUMBER ZERO WITHOUT ANY GAPS TO CLARIFY THE EXPRESSION TAGS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HNCA
1413D CBCA(CO)NH
1513D HNCO
2623D CC(CO)NH
2723D HCC(CO)NH
2823D 15N-edited NOESY
2923D 13C-edited NOESY
21023D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-13C; U-15N] katanin p60; 20mM sodium phosphate; 1mM EDTA; 95% H2O/5% D2O95% H2O/5% D2O
20.7mM [U-13C; U-15N] katanin p60; 20mM sodium phosphate; 50mM sodium chloride; 1mM EDTA; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMkatanin p60[U-13C; U-15N]1
20 mMsodium phosphate1
1 mMEDTA1
0.7 mMkatanin p60[U-13C; U-15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMEDTA2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 6.5 ambient 298 K
270 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
MOLMOL2K.2Koradi, Billeter and Wuthrichchemical shift assignment
MOLMOL2K.2Koradi, Billeter and Wuthrichrefinement
Sparky3.106Goddardrefinement
Sparky3.106Goddardchemical shift assignment
XwinNMR3.5Bruker Biospincollection
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: distance geometry, rigid body restrained molecular dynamics, dihedral angle molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 11

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