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- PDB-5h7p: NMR structure of the Vta1NTD-Did2(176-204) complex -

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Basic information

Entry
Database: PDB / ID: 5h7p
TitleNMR structure of the Vta1NTD-Did2(176-204) complex
Components
  • Vacuolar protein sorting-associated protein VTA1Vacuole
  • Vacuolar protein-sorting-associated protein 46Vacuole
KeywordsPROTEIN TRANSPORT / Endosomal Sorting Complexes Required for Transport / Multivesicular Bodies / microtubule-interacting and transport (MIT) domain / MIT-interacting motif 1 (MIM1) / Saccharomyces cerevisiae Proteins
Function / homology
Function and homology information


ESCRT III complex assembly / ESCRT IV complex / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / lipid transport / ATPase activator activity / multivesicular body ...ESCRT III complex assembly / ESCRT IV complex / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / lipid transport / ATPase activator activity / multivesicular body / protein-macromolecule adaptor activity / late endosome / protein transport / endosome / cytoplasm
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 46 / Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model6
AuthorsShen, J. / Yang, Z. / Wild, C.J.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China2011CB966300 China
Science and Technology Commission of Shanghai Municipality15ZR1449300 China
CitationJournal: Sci Rep / Year: 2016
Title: NMR studies on the interactions between yeast Vta1 and Did2 during the multivesicular bodies sorting pathway
Authors: Shen, J. / Yang, Z. / Wang, J. / Zhao, B. / Lan, W. / Wang, C. / Zhang, X. / Wild, C.J. / Liu, M. / Xu, Z. / Cao, C.
History
DepositionNov 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 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 46


Theoretical massNumber of molelcules
Total (without water)22,4042
Polymers22,4042
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 / Fragment: UNP residues 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: VTA1, YLR181C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06263
#2: Protein/peptide Vacuolar protein-sorting-associated protein 46 / Vacuole / Charged multivesicular body protein 1 / DOA4-independent degradation protein 2 / Fifty two inhibitor 1


Mass: 3341.793 Da / Num. of mol.: 1 / Fragment: UNP residues 176-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: DID2, CHM1, FTI1, VPS46, YKR035W-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69771

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic12D 1H-13C HSQC aromatic
131isotropic22D 1H-15N HSQC
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-15N NOESY
1111isotropic13D (H)CCH-TOCSY
1122isotropic13D HNCO
1132isotropic13D HN(CA)CB
1142isotropic13D CBCA(CO)NH
1152isotropic13D (H)CCH-TOCSY
1161isotropic13D 13C-F1 edited NOESY
1172isotropic13D 13C-F1 edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution125 mM NA- sodium phosphate-1, 100 mM NA- sodium chloride-2, 5 mM [U-100% 2H] DTT-3, 10 % [U-100% 2H] D2O-4, 0.02 % NA- sodium azide-5, 90% H2O/10% D2Odouble labeled vta1NTD with unlabeled Did2 peptide15N,13C90% H2O/10% D2O
solution225 mM NA- sodium phosphate-1, 100 mM NA- sodium chloride-2, 5 mM [U-100% 2H] DTT-3, 10 % [U-100% 2H] D2O-4, 0.02 % NA- sodium azide-5, 90% H2O/10% D2O15N,13C and 70% 2H labeled vta1NTD with unlabeled Did2 peptide15N,13C,2H90% H2O/10% D2O
solution325 mM NA- sodium phosphate-1, 100 mM NA- sodium chloride-2, 5 mM [U-100% 2H] DTT-3, 10 % [U-100% 2H] D2O-4, 0.02 % NA- sodium azide-5, 90% H2O/10% D2O15N,13C double labeled Did2 peptide with unlabeled Vta1NTD15N, 13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-1NA-1
100 mMsodium chloride-2NA-1
5 mMDTT-3[U-100% 2H]1
10 %D2O-4[U-100% 2H]1
0.02 %sodium azide-5NA-1
25 mMsodium phosphate-1NA-2
100 mMsodium chloride-2NA-2
5 mMDTT-3[U-100% 2H]2
10 %D2O-4[U-100% 2H]2
0.02 %sodium azide-5NA-2
25 mMsodium phosphate-1NA-3
100 mMsodium chloride-2NA-3
5 mMDTT-3[U-100% 2H]3
10 %D2O-4[U-100% 2H]3
0.02 %sodium azide-5NA-3
Sample conditionsIonic strength: 175 mM / Label: conditon-1 / pH: 7.0 / Pressure: ambient atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE8001with cryo-probe
Varian Unity InovaVarianUnity Inova6002with cryo-probe

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Processing

NMR software
NameVersionDeveloperClassification
SparkySparky 3T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Franciscochemical shift assignment
XPLOR-NIHC.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore, "The Xplor-NIH NMR Molecular Structure Determination Package," J. Magn. Res., 160, 66-74 (2003).refinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 6

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