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- PDB-7jsq: Refined structure of the C-terminal domain of DNAJB6b -

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Basic information

Entry
Database: PDB / ID: 7jsq
TitleRefined structure of the C-terminal domain of DNAJB6b
ComponentsDnaJ homolog subfamily B member 6
KeywordsCHAPERONE / anti-aggregation / hsp40
Function / homology
Function and homology information


chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / regulation of cellular response to heat / chaperone-mediated protein folding ...chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / regulation of cellular response to heat / chaperone-mediated protein folding / heat shock protein binding / protein folding chaperone / Hsp70 protein binding / extracellular matrix organization / : / Z disc / unfolded protein binding / protein folding / regulation of protein localization / protein-folding chaperone binding / actin cytoskeleton organization / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
DnaJ homolog subfamily B member 2 / 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
DnaJ homolog subfamily B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKaramanos, T.K. / Clore, G.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK-029023 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: An S/T motif controls reversible oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of a beta sheet backbone.
Authors: Karamanos, T.K. / Tugarinov, V. / Clore, G.M.
History
DepositionAug 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 6


Theoretical massNumber of molelcules
Total (without water)6,4741
Polymers6,4741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily B member 6 / HHDJ1 / Heat shock protein J2 / HSJ-2 / MRJ / MSJ-1


Mass: 6474.404 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 185-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB6, HSJ2, MRJ, MSJ1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75190

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
161isotropic1HAHBCONH
121isotropic33D HHC-NOESY
131isotropic23D HCC-NOESY
171isotropic3CNH 13C-HMQC-NOESY-15N-HSQC
142anisotropic1IPAP HSQC
152anisotropic1JMOD 1H13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.2 mM [U-13C; U-15N] CTD, 20 mM sodium phosphate, 150 mM sodium chloride, 0.02 % v/v sodium azide, 95% H2O/5% D2OU13C_U15N_sample95% H2O/5% D2O
solution20.2 mM [U-13C; U-15N] CTD, 20 mM sodium phosphate, 150 mM sodium chloride, 0.02 % v/v sodium azide, 4.2 % v/v C12E5 PEG, 11.6 mM Hexanol, 95% H2O/5% D2ORDC_sample95% H2O/5% D2OPEG/hexanol sample
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMCTD[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.02 % v/vsodium azidenatural abundance1
0.2 mMCTD[U-13C; U-15N]2
20 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.02 % v/vsodium azidenatural abundance2
4.2 % v/vC12E5 PEGnatural abundance2
11.6 mMHexanolnatural abundance2
Sample conditionsIonic strength: 187 mM / Label: condition_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE III HDBrukerAVANCE III HD7002
Bruker AVANCE III HDBrukerAVANCE III HD9003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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