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- PDB-1wr0: Structural characterization of the MIT domain from human Vps4b -

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Basic information

Entry
Database: PDB / ID: 1wr0
TitleStructural characterization of the MIT domain from human Vps4b
ComponentsSKD1 protein
KeywordsPROTEIN TRANSPORT / VPS4b / SKD1 / MIT DOMAIN / ESCORT / MVB / SNPs / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / ESCRT III complex disassembly / late endosomal microautophagy / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission ...protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / ESCRT III complex disassembly / late endosomal microautophagy / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission / establishment of blood-brain barrier / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / cholesterol transport / endosome to lysosome transport via multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / vesicle-fusing ATPase / Flemming body / nucleus organization / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / response to lipid / viral budding via host ESCRT complex / autophagosome maturation / canonical Wnt signaling pathway / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / positive regulation of G2/M transition of mitotic cell cycle / viral budding from plasma membrane / macroautophagy / Budding and maturation of HIV virion / potassium ion transport / autophagy / spindle pole / protein transport / late endosome membrane / midbody / angiogenesis / endosome membrane / endosome / centrosome / protein-containing complex binding / ATP hydrolysis activity / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / 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
Vacuolar protein sorting-associated protein 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics, energy minimization
AuthorsTakasu, H. / Jee, J.G. / Ohno, A. / Goda, N. / Fujiwara, K. / Tochio, H. / Shirakawa, M. / Hiroaki, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Structural characterization of the MIT domain from human Vps4b
Authors: Takasu, H. / Jee, J.G. / Ohno, A. / Goda, N. / Fujiwara, K. / Tochio, H. / Shirakawa, M. / Hiroaki, H.
History
DepositionOct 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 2, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SKD1 protein


Theoretical massNumber of molelcules
Total (without water)9,2071
Polymers9,2071
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 / 94structures with the lowest energy
Representative

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Components

#1: Protein SKD1 protein / Vacuolar sorting protein 4b


Mass: 9207.310 Da / Num. of mol.: 1 / Fragment: MIT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRESAT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75351

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM protein U-15N; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT95% H2O/5% D2O
21mM protein U-15N,13C; 20mM Tris buffer; 50mM NaCl; 95% H2O, 5% D2O; 1mM DTT95% H2O/5% D2O
Sample conditionsIonic strength: NaCl 50mM / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipe2.1Delaglioprocessing
Sparky3.11Goddarddata analysis
CYANA2Guntertstructure solution
Amber7Pearlmanrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics, energy minimization
Software ordinal: 1
Details: the structures are based on a total of 1539 restraints, 1471 are NOE-derived distance constraints, 68 dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 94 / Conformers submitted total number: 20

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