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

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Basic information

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


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / : / phosphoprotein phosphatase activity / protein dephosphorylation / unfolded protein binding / outer membrane-bounded periplasmic space / protein refolding ...oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / : / phosphoprotein phosphatase activity / protein dephosphorylation / unfolded protein binding / outer membrane-bounded periplasmic space / protein refolding / periplasmic space / DNA replication / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Nt-dnaJ domain signature. / DnaJ domain, conserved site ...HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Alkaline phosphatase / Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus 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 1.3May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline phosphatase,Chaperone protein DnaJ 2 fusion


Theoretical massNumber of molelcules
Total (without water)16,6251
Polymers16,6251
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 Alkaline phosphatase,Chaperone protein DnaJ 2 fusion / APase


Mass: 16625.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: K12, HB8 / ATCC 27634 / DSM 579 / Gene: phoA, b0383, JW0374, dnaJ2, TTHA1489 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P00634, UniProt: Q56237, alkaline phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HMQC
142isotropic13D HN(CA)CB
1141isotropic13D 1H-15N NOESY
1131isotropic13D CCH-SFNOESY
1121isotropic13D NCH-SFNOESY
1111isotropic13D CNH-SFNOESY
1101isotropic13D HCH-SFNOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [ILVMAT-sel-1H-13C_methyls; U-15N; U-2H] C-CBD1-CBD2, 75 mM potassium chloride, 20 mM potassium phosphate, 0.04 % sodium azide, 90% H2O/10% D2Ohighly deuterated with all methyls U-1H-13C for 3D NOESYsU-2H_15N_ILVMAT_sel_1H-13Cmethyl90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] C-CBD1-CBD2, 75 mM potassium chloride, 20 mM potassium phosphate, 0.04 % sodium azide, 90% H2O/10% D2Odouble labeled for backbone15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-CBD1-CBD2[ILVMAT-sel-1H-13C_methyls; U-15N; U-2H]1
75 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.04 %sodium azidenatural abundance1
1 mMC-CBD1-CBD2[U-100% 13C; U-100% 15N]2
75 mMpotassium chloridenatural abundance2
20 mMpotassium phosphatenatural abundance2
0.04 %sodium azidenatural abundance2
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
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
TopSpin4Bruker Biospincollection
PSVSBhattacharya and Montelionegeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: restrained MD in 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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