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- PDB-9dyv: Assembly and functional mechanisms of the Hsp70-Hsp40 chaperone m... -

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Basic information

Entry
Database: PDB / ID: 9dyv
TitleAssembly and functional mechanisms of the Hsp70-Hsp40 chaperone machinery
ComponentsChaperone protein DnaJ 2
KeywordsSTRUCTURAL PROTEIN / DnaJ
Function / homology
Function and homology information


: / unfolded protein binding / protein refolding / DNA replication / cytoplasm
Similarity search - Function
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
Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsJiang, Y. / Ibrahim, Z. / Xia, Y. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM122462 United States
CitationJournal: Mol.Cell / Year: 2025
Title: Mechanisms of assembly and function of the Hsp70-Hsp40 chaperone machinery
Authors: Jiang, Y. / Ibrahim, Z. / Xia, Y. / Clay, M. / Myasnikov, A. / Immadisetty, K. / Xia, Z. / Tang, L. / Rossi, P. / Ganguly, P. / Liu, J. / Miller, D. / Che, M. / Palacios, S.M. / Kramer, G. / ...Authors: Jiang, Y. / Ibrahim, Z. / Xia, Y. / Clay, M. / Myasnikov, A. / Immadisetty, K. / Xia, Z. / Tang, L. / Rossi, P. / Ganguly, P. / Liu, J. / Miller, D. / Che, M. / Palacios, S.M. / Kramer, G. / Bukau, B. / Kalodimos, C.G.
History
DepositionOct 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein DnaJ 2


Theoretical massNumber of molelcules
Total (without water)13,4331
Polymers13,4331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Chaperone protein DnaJ 2


Mass: 13432.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: dnaJ2, TTHA1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56237
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D (H)CCH-COSY
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 500 uM 13C/15N labeled DnaJ1-116, 5 % 2H-labeled D2O, 100 mM NaCl, 50 mM Phosphate Buffer System, 95 % H2O, 90% H2O/10% D2O
Details: 500 uM 13C/15N-labeled DnaJ1-116 in PBS buffer / Label: DnaJ / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMDnaJ1-11613C/15N labeled1
5 %D2O2H-labeled1
100 mMNaClnatural abundance1
50 mMPhosphate Buffer Systemnatural abundance1
95 %H2Onatural abundance1
Sample conditionsIonic strength: 150 mM / Label: condition1 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO7001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JLchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRFAM-SPARKYLee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JLpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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