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- PDB-5vso: NMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 5vso
TitleNMR structure of Ydj1 J-domain, a cytosolic Hsp40 from Saccharomyces cerevisiae
ComponentsYeast dnaJ protein 1
KeywordsCHAPERONE / J-domain / J-protein / DnaJ
Function / homology
Function and homology information


tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to ER / response to oxygen levels / protein targeting to mitochondrion / 'de novo' protein folding / ATPase activator activity / chaperone-mediated protein complex assembly / ERAD pathway ...tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to ER / response to oxygen levels / protein targeting to mitochondrion / 'de novo' protein folding / ATPase activator activity / chaperone-mediated protein complex assembly / ERAD pathway / transcription repressor complex / Hsp70 protein binding / cellular response to starvation / unfolded protein binding / protein transport / protein-folding chaperone binding / cellular response to heat / protein refolding / ubiquitin-dependent protein catabolic process / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. ...DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
Mitochondrial protein import protein MAS5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsCiesielski, S.J. / Tonelli, M. / Lee, W. / Cornilescu, G. / Markley, J.L. / Schilke, B.A. / Ziegelhoffer, T. / Craig, E.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM31107 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM27870 United States
CitationJournal: PLoS Genet. / Year: 2017
Title: Broadening the functionality of a J-protein/Hsp70 molecular chaperone system.
Authors: Schilke, B.A. / Ciesielski, S.J. / Ziegelhoffer, T. / Kamiya, E. / Tonelli, M. / Lee, W. / Cornilescu, G. / Hines, J.K. / Markley, J.L. / Craig, E.A.
History
DepositionMay 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: Yeast dnaJ protein 1


Theoretical massNumber of molelcules
Total (without water)8,5221
Polymers8,5221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5280 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Yeast dnaJ protein 1 / Ydj1 / Mitochondrial protein import protein MAS5


Mass: 8521.567 Da / Num. of mol.: 1 / Fragment: residues 1-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YDJ1, MAS5, YNL064C, N2418, YNL2418C / Production host: Escherichia coli (E. coli) / References: UniProt: P25491

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic32D 1H-13C HSQC aliphatic
131isotropic32D 1H-13C HSQC aromatic
141isotropic33D (H)CCH-TOCSY
1161isotropic23D CBCA(CO)NH
1171isotropic23D HN(CA)CB
1181isotropic33D HNCO
151isotropic33D HBHA(CO)NH
1101isotropic33D C(CO)NH
191isotropic33D H(CCO)NH
181isotropic13D 1H-13C NOESY aliphatic
172isotropic13D 1H-13C NOESY aromatic
1132isotropic32D 1H-15N HSQC
1113isotropic32D 1H-15N HSQC
2123isotropic32D 1H-15N HSQC
2144anisotropic42D 1H-15N HSQC
2154isotropic42D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDLabelSolvent system
solution115N 13C93% H2O/7% D2O
solution215N 13C93% H2O/7% D2O
solution315N93% H2O/7% D2O
gel solid415N93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.5 mg/mLYdj1 protein (1-70 residues)[U-15N] [U-13C]1
4.0 mg/mLYdj1 protein (1-70 residues)[U-15N] [U-13C]2
5.5 mg/mLYdj1 protein (1-70 residues)[U-15N]3
5.5 mg/mLYdj1 protein (1-70 residues)[U-15N]4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM Tris, pH 7.5, 150 mM NaCl, 5 mM DTT with protease inhibitor tablets and 0.2% NaN3150 NaCl mMconditions_17.51 atm279 K
220 mM Tris, pH 7.5, 150 mM NaCl, 5 mM DTT with protease inhibitor tablets and 0.2% NaN3150 NaCl mMconditions_27.51 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9001
Varian VXRSVarianVXRS8002
Varian VXRSVarianVXRS6003
Bruker AVANCE IIIBrukerAVANCE III6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKY1.41Lee, Tonelli and Markleypeak picking
APESShin, Lee and Leepeak picking
NMRFAM-SPARKY1.41Lee, Tonelli and Markleychemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PINE-SPARKYLee, Westler, Bahrami, Eghbalnia and Markleychemical shift assignment
PONDEROSA-C/SLee, Stark and Markleystructure calculation
AUDANALee, Petit, Cornilescu, Stark and Markleystructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Stark and Markleyrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 12 / Details: Final step with explicit water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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