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- PDB-2luh: NMR structure of the Vta1-Vps60 complex -

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Basic information

Entry
Database: PDB / ID: 2luh
TitleNMR structure of the Vta1-Vps60 complex
Components
  • Vacuolar protein sorting-associated protein VTA1Vacuole
  • Vacuolar protein-sorting-associated protein 60Vacuole
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / Vta1 / Vps60 / ESCRT / MVB / Novel MIT recognition mode
Function / homology
Function and homology information


ESCRT IV complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / filamentous growth / vesicle budding from membrane / late endosome to vacuole transport / fungal-type vacuole membrane / lipid transport / ATPase activator activity / multivesicular body ...ESCRT IV complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / filamentous growth / vesicle budding from membrane / late endosome to vacuole transport / fungal-type vacuole membrane / lipid transport / ATPase activator activity / multivesicular body / protein transport / protein-macromolecule adaptor activity / endosome membrane / endosome / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1710 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1710 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 60 / Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Z. / Vild, C. / Ju, J. / Zhang, X. / Liu, J. / Shen, J. / Zhao, B. / Lan, W. / Gong, F. / Liu, M. ...Yang, Z. / Vild, C. / Ju, J. / Zhang, X. / Liu, J. / Shen, J. / Zhao, B. / Lan, W. / Gong, F. / Liu, M. / Cao, C. / Xu, Z.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Basis of Molecular Recognition between ESCRT-III-like Protein Vps60 and AAA-ATPase Regulator Vta1 in the Multivesicular Body Pathway.
Authors: Yang, Z. / Vild, C. / Ju, J. / Zhang, X. / Liu, J. / Shen, J. / Zhao, B. / Lan, W. / Gong, F. / Liu, M. / Cao, C. / Xu, Z.
History
DepositionJun 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references
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
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
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
B: Vacuolar protein-sorting-associated protein 60


Theoretical massNumber of molelcules
Total (without water)25,6712
Polymers25,6712
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Vacuolar protein sorting-associated protein VTA1 / Vacuole / VPS20-associated protein 1


Mass: 19062.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VTA1, YLR181C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q06263
#2: Protein Vacuolar protein-sorting-associated protein 60 / Vacuole / Charged multivesicular body protein 5


Mass: 6609.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VPS60, CHM5, MOS10, YDR486C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q03390

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1322D 1H-13C HSQC aliphatic
1442D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aromatic
1642D 1H-13C HSQC aromatic
1713D CBCA(CO)NH
1833D CBCA(CO)NH
1913D HNCO
11033D HNCO
11113D HNCA
11233D HNCA
11313D HN(CA)CB
11433D HN(CA)CB
11513D HN(CO)CA
11633D HN(CO)CA
11723D (H)CCH-TOCSY
11843D (H)CCH-TOCSY
11913D 1H-15N NOESY
12033D 1H-15N NOESY
12123D 1H-13C NOESY aliphatic
12243D 1H-13C NOESY aliphatic
12323D 1H-13C NOESY aromatic
12443D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-1.2 mM [U-13C; U-15N] protein_1, 1.0-1.2 mM protein_2, 90% H2O/10% D2O90% H2O/10% D2O
21.0-1.2 mM [U-13C; U-15N] protein_1, 1.0-1.2 mM protein_2, 100% D2O100% D2O
31.0-1.2 mM protein_1, 1.0-1.2 mM [U-13C; U-15N] protein_2, 90% H2O/10% D2O90% H2O/10% D2O
41.0-1.2 mM protein_1, 1.0-1.2 mM [U-13C; U-15N] protein_2, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]1.0-1.21
mMentity_2-21.0-1.21
mMentity_1-3[U-13C; U-15N]1.0-1.22
mMentity_2-41.0-1.22
mMentity_1-51.0-1.23
mMentity_2-6[U-13C; U-15N]1.0-1.23
mMentity_1-71.0-1.24
mMentity_2-8[U-13C; U-15N]1.0-1.24
Sample conditionsIonic strength: 0.15 / pH: 7.0 / Pressure: ambient / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHNIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHNIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
ProcheckNMRLaskowski and MacArthurstructure analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 4471 / NOE intraresidue total count: 1215 / NOE long range total count: 659 / NOE medium range total count: 1340 / NOE sequential total count: 971 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 195 / Protein psi angle constraints total count: 195
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.023 Å / Distance rms dev error: 0.00053 Å

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