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- PDB-1yxr: NMR Structure of VPS4A MIT Domain -

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Basic information

Entry
Database: PDB / ID: 1yxr
TitleNMR Structure of VPS4A MIT Domain
Componentsvacuolar protein sorting factor 4A
KeywordsPROTEIN TRAFFICKING / VPS4 / MIT domain
Function / homology
Function and homology information


vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / late endosomal microautophagy / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / endosomal vesicle fusion / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / late endosomal microautophagy / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / endosomal vesicle fusion / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport / : / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / nuclear envelope organization / nuclear membrane reassembly / mitotic nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane fission / positive regulation of exosomal secretion / ATP-dependent protein disaggregase activity / vesicle budding from membrane / multivesicular body assembly / protein targeting to lysosome / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / plasma membrane repair / Flemming body / vacuolar membrane / vesicle-fusing ATPase / endosomal transport / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / viral release from host cell / autophagosome maturation / regulation of protein localization to plasma membrane / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Budding and maturation of HIV virion / autophagy / spindle pole / late endosome / late endosome membrane / regulation of protein localization / midbody / early endosome / lysosome / endosome / endosome membrane / cell division / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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 ...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 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / automated NOE assignment using CYANA, torsion angle dynamics for structure calculations
AuthorsScott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I.
CitationJournal: To be Published
Title: NMR Structure of VPS4A MIT Domain
Authors: Scott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: vacuolar protein sorting factor 4A


Theoretical massNumber of molelcules
Total (without water)9,0561
Polymers9,0561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #18lowest energy

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Components

#1: Protein vacuolar protein sorting factor 4A / VPS4A / SKD1 protein


Mass: 9056.336 Da / Num. of mol.: 1 / Fragment: MIT Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: pET16b reengineered to contain a TEV cleavage site in place of the normal factor Xa site
Gene: 27183 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UN37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: Uniform labeling with 15N and 13C. / Solvent system: 50 mM NaCl, 20 mM sodium phosphate, 10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Accelyrs, San Diegoprocessing
Sparky3.11TD Goddard and DG Knellerdata analysis
CYANA2P Guntertstructure solution
CNS1.1AT Brunger, et al.refinement
RefinementMethod: automated NOE assignment using CYANA, torsion angle dynamics for structure calculations
Software ordinal: 1
Details: The structures are based on 1432 NOE derived distance constraints, 150 dihedral angle constraints (generated by TALOS) and 114 distance constraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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