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- PDB-2lxm: Lip5-chmp5 -

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Basic information

Entry
Database: PDB / ID: 2lxm
TitleLip5-chmp5
Components
  • Charged multivesicular body protein 5
  • Vacuolar protein sorting-associated protein VTA1 homologVacuole
KeywordsPROTEIN TRANSPORT / MIT
Function / homology
Function and homology information


amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / cellular response to muramyl dipeptide ...amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / cellular response to muramyl dipeptide / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vesicle budding from membrane / membrane fission / plasma membrane repair / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / regulation of receptor recycling / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / erythrocyte differentiation / viral budding from plasma membrane / macroautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / midbody / cellular response to lipopolysaccharide / endosome membrane / cadherin binding / lysosomal membrane / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / 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 / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...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 / Snf7 family / Snf7 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein VTA1 homolog / Charged multivesicular body protein 5
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 1.2Apr 27, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VTA1 homolog
B: Charged multivesicular body protein 5


Theoretical massNumber of molelcules
Total (without water)25,5122
Polymers25,5122
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 / 500structures 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: 19215.205 Da / Num. of mol.: 1 / Fragment: UNP residues 1-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C6orf55, HSPC228, My012, VTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP79
#2: Protein Charged multivesicular body protein 5 / Chromatin-modifying protein 5 / SNF7 domain-containing protein 2 / Vacuolar protein sorting- ...Chromatin-modifying protein 5 / SNF7 domain-containing protein 2 / Vacuolar protein sorting-associated protein 60 / Vps60 / hVps60


Mass: 6296.492 Da / Num. of mol.: 1 / Fragment: UNP residues 139-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: C9orf83, CGI-34, CHMP5, HSPC177, PNAS-114, PNAS-2, SNF7DC2
Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZZ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-13C NOESY aromatic
1312D 1H-15N HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D HNHA
11113D H(CCO)NH
11213D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] LIP5(1-168), 0.5 mM [U-100% 13C; U-100% 15N] CHMP5(139-195), 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
0.5 mMLIP5(1-168)-1[U-100% 13C; U-100% 15N]1
0.5 mMCHMP5(139-195)-2[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-31
50 mMsodium chloride-41
0.5 mMDTT-51
0.1 mMEDTA-61
Sample conditionsIonic strength: 75 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian DirectDriveVarianDirect Drive9002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddarddata analysis
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: 500 / Conformers submitted total number: 10

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