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- PDB-2lxl: Lip5(mit)2 -

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Basic information

Entry
Database: PDB / ID: 2lxl
TitleLip5(mit)2
ComponentsVacuolar protein sorting-associated protein VTA1 homologVacuole
KeywordsPROTEIN TRANSPORT / MIT
Function / homology
Function and homology information


ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / multivesicular body sorting pathway / multivesicular body assembly / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / macroautophagy / Budding and maturation of HIV virion / protein transport / endosome membrane ...ESCRT III complex disassembly / late endosome to vacuole transport via multivesicular body sorting pathway / multivesicular body sorting pathway / multivesicular body assembly / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / macroautophagy / Budding and maturation of HIV virion / protein transport / endosome membrane / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein vta1 / Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein VTA1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsSkalicky, J.J. / Sundquist, W.I.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Interactions of the Human LIP5 Regulatory Protein with Endosomal Sorting Complexes Required for Transport.
Authors: Skalicky, J.J. / Arii, J. / Wenzel, D.M. / Stubblefield, W.M. / Katsuyama, A. / Uter, N.T. / Bajorek, M. / Myszka, D.G. / Sundquist, W.I.
History
DepositionAug 29, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VTA1 homolog


Theoretical massNumber of molelcules
Total (without water)20,8601
Polymers20,8601
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)10 / 400structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Vacuolar protein sorting-associated protein VTA1 homolog / Vacuole / Dopamine-responsive gene 1 protein / DRG-1 / LYST-interacting protein 5 / LIP5 / SKD1-binding protein 1 / SBP1


Mass: 20859.770 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTA1, C6orf55, HSPC228, My012 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP79

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic
1412D 1H-15N HSQC
1512D 1H-13C HSQC aliphatic
1612D 1H-13C HSQC aromatic
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] LIP5(1-183), 25 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM DTT, 0.1 mM EDTA, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMLIP5(1-183)-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
50 mMsodium chloride-31
0.5 mMDTT-41
0.1 mMEDTA-51
Sample conditionsIonic strength: 0.075 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ113Variancollection
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 10

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