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- PDB-6prp: Structural Basis for Client Recognition and Activity of Hsp40 Cha... -

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Basic information

Entry
Database: PDB / ID: 6prp
TitleStructural Basis for Client Recognition and Activity of Hsp40 Chaperones
ComponentsChaperone protein DnaK, Chaperone protein DnaJ 2 fusion
KeywordsCHAPERONE / HYDROLASE / Client Recognition
Function / homology
Function and homology information


chaperone cofactor-dependent protein refolding / unfolded protein binding / protein folding / protein refolding / DNA replication / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Chaperone DnaK / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily ...HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Chaperone DnaK / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chaperone protein DnaK / Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsJiang, Y. / Rossi, P. / Kalodimos, C.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM122462-04 United States
CitationJournal: Science / Year: 2019
Title: Structural basis for client recognition and activity of Hsp40 chaperones.
Authors: Jiang, Y. / Rossi, P. / Kalodimos, C.G.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: Chaperone protein DnaK, Chaperone protein DnaJ 2 fusion


Theoretical massNumber of molelcules
Total (without water)9,1761
Polymers9,1761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, NMR titrations
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Chaperone protein DnaK, Chaperone protein DnaJ 2 fusion


Mass: 9176.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria), (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: dnaJ2, TTHA1489 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q56237, UniProt: Q56235*PLUS, alkaline phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HBHA(CO)NH
1121isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY
1101isotropic13D CCH-NOESY
191isotropic13D CaroCH-NOESY
181isotropic13D CCH-TOCSY
171isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] DnaK-ctail-CBD2, 75 mM potassium chloride, 20 mM potassium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O
Details: double labeled fusion / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDnaK-ctail-CBD2[U-100% 13C; U-100% 15N]1
75 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.04 %sodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionegeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: restrained MD in explicit H2O
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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