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- PDB-7qby: Refined structure of the T193A mutant in the C-terminal domain of... -

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Basic information

Entry
Database: PDB / ID: 7qby
TitleRefined structure of the T193A mutant in the C-terminal domain of DNAJB6b
ComponentsIsoform B of DnaJ homolog subfamily B member 6
KeywordsCHAPERONE / Hsp40 chaperone / anti-aggregation
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 / chaperone-mediated protein folding / regulation of cellular response to heat ...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 / chaperone-mediated protein folding / regulation of cellular response to heat / protein folding chaperone / Hsp70 protein binding / heat shock protein binding / extracellular matrix organization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Z disc / regulation of protein localization / unfolded protein binding / protein folding / protein-folding chaperone binding / actin cytoskeleton organization / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol
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. / Cawood, E.E.
Funding support United States, 3items
OrganizationGrant numberCountry
Wellcome Trust223268/Z/21/Z United States
Other private1520 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK-029023 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Microsecond Backbone Motions Modulate the Oligomerization of the DNAJB6 Chaperone.
Authors: Cawood, E.E. / Clore, G.M. / Karamanos, T.K.
History
DepositionNov 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 19, 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: Isoform B of DnaJ homolog subfamily B member 6


Theoretical massNumber of molelcules
Total (without water)6,4441
Polymers6,4441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #11

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Components

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


Mass: 6444.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C terminal domain of DNAJB6b including the T193A mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB6, HSJ2, MRJ, MSJ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 1H-13C NOESY HCH
121isotropic13D 1H-13C NOESY CCH
131isotropic1JHNHA ARTSY
141isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 0.2 mM [U-13C; U-15N] DNAJ HOMOLOG SUBFAMILY B MEMBER 6 C-TERMINAL DOMAIN, 20 mM sodium phosphate, 150 mM sodium chloride, 0.02 % v/v sodium azide, 95% H2O/5% D2O
Label: 13C15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDNAJ HOMOLOG SUBFAMILY B MEMBER 6 C-TERMINAL DOMAIN[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.02 % v/vsodium azidenatural abundance1
Sample conditionsIonic strength: 87 mM / Label: condition_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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