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- PDB-2jqh: VPS4B MIT -

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Basic information

Entry
Database: PDB / ID: 2jqh
TitleVPS4B MIT
ComponentsVacuolar protein sorting-associating protein 4B
KeywordsPROTEIN TRANSPORT / VPS4B / MIT / Three Helix Bundle
Function / homology
Function and homology information


protein depolymerization / late endosomal microautophagy / 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 / regulation of centrosome duplication / nuclear membrane reassembly / establishment of blood-brain barrier ...protein depolymerization / late endosomal microautophagy / 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 / regulation of centrosome duplication / nuclear membrane reassembly / establishment of blood-brain barrier / multivesicular body sorting pathway / vacuole organization / plasma membrane repair / positive regulation of exosomal secretion / midbody abscission / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endosome to lysosome transport via multivesicular body sorting pathway / cholesterol transport / regulation of mitotic spindle assembly / Flemming body / vesicle-fusing ATPase / endosomal transport / mitotic metaphase chromosome alignment / response to lipid / nucleus organization / ATPase complex / viral budding via host ESCRT complex / autophagosome maturation / canonical Wnt signaling pathway / nuclear pore / positive regulation of G2/M transition of mitotic cell cycle / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / macroautophagy / potassium ion transport / Budding and maturation of HIV virion / autophagy / spindle pole / late endosome membrane / protein transport / midbody / angiogenesis / endosome / endosome membrane / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / centrosome / protein-containing complex binding / protein homodimerization activity / ATP hydrolysis 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 ...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 / simulated annealing
AuthorsStuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Ghaffarian, S. / Sundquist, W.I.
CitationJournal: Nature / Year: 2007
Title: ESCRT-III recognition by VPS4 ATPases.
Authors: Stuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Karren, M.A. / Ghaffarian, S. / Sundquist, W.I.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associating protein 4B


Theoretical massNumber of molelcules
Total (without water)10,1931
Polymers10,1931
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vacuolar protein sorting-associating protein 4B / Suppressor of K+ / transport growth defect 1 / Protein SKD1


Mass: 10192.597 Da / Num. of mol.: 1 / Fragment: MIT domain, residues 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4B, SKD1, VPS42 / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D HNHA
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11213D 1H-15N NOESY
NMR detailsText: Half-filtered NOESYs provided the intermolecular NOEs

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Sample preparation

DetailsContents: 1.8 mM [U-100% 13C; U-100% 15N] VPS4B MIT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.8 mM / Component: VPS4B MIT / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 5.65 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2004Accelrys Software Inc.processing
Sparky3.112Goddardchemical shift assignment
Sparky3.112Goddardpeak picking
Sparky3.112Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Refinement using anneal.inp and using summed NOE constraints with max T of 3000 K for simulated annealing.
NMR constraintsNOE constraints total: 1769 / NOE intraresidue total count: 426 / NOE long range total count: 387 / NOE medium range total count: 538 / NOE sequential total count: 418 / Hydrogen bond constraints total count: 55 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 60 / Protein psi angle constraints total count: 60
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.03 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.1 ° / Maximum upper distance constraint violation: 0.065 Å / Torsion angle constraint violation method: CNS
NMR ensemble rmsDistance rms dev: 0.004 Å

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