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- PDB-6d6x: HSP40 co-chaperone Sis1 J-domain -

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Basic information

Entry
Database: PDB / ID: 6d6x
TitleHSP40 co-chaperone Sis1 J-domain
ComponentsType II HSP40 co-chaperone
KeywordsCHAPERONE / Sis1 / J-domain
Function / homology
Function and homology information


tRNA import into nucleus / : / Regulation of HSF1-mediated heat shock response / misfolded protein transport / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding ...tRNA import into nucleus / : / Regulation of HSF1-mediated heat shock response / misfolded protein transport / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding / translational initiation / cytosolic small ribosomal subunit / unfolded protein binding / protein folding / protein-folding chaperone binding / cell cycle / DNA binding / nucleus / cytosol
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / de novo
AuthorsPinheiro, G.M.S. / Amorim, G.C. / Iqbal, A. / Ramos, C.H.I. / Almeida, F.C.L.
Funding support Brazil, 6items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/50161-8 Brazil
Sao Paulo Research Foundation (FAPESP)2017/01074-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)Produtividade em Pesquisa 209306/2013-2 Brazil
Other governmentCientista do Nosso Estado 215141 Brazil
Other government210361 Brazil
Other governmentPensa Rio 204432 Brazil
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: Solution NMR investigation on the structure and function of the isolated J-domain from Sis1: Evidence of transient inter-domain interactions in the full-length protein.
Authors: Pinheiro, G.M.S. / Amorim, G.C. / Iqbal, A. / Almeida, F.C.L. / Ramos, C.H.I.
History
DepositionApr 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 12, 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type II HSP40 co-chaperone


Theoretical massNumber of molelcules
Total (without water)9,0911
Polymers9,0911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5340 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Type II HSP40 co-chaperone


Mass: 9091.122 Da / Num. of mol.: 1 / Fragment: residues 2-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIS1, SCKG_3227 / Plasmid: pEt32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A250WHC7, UniProt: P25294*PLUS

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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
171isotropic12D 1H-13C HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
182isotropic23D 1H-15N NOESY
191isotropic23D 1H-13C NOESY
1101isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1220 uM [U-13C; U-15N] Sis1 1-81, 90% H2O/10% D2O15N, 13C90% H2O/10% D2O
solution2200 uM [U-15N] Sis1 1-81, 90% H2O/10% D2O15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
220 uMSis1 1-81[U-13C; U-15N]1
200 uMSis1 1-81[U-15N]2
Sample conditionsIonic strength: 200 mM / Label: 1 / pH: 7.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AnalysisCCPNchemical shift assignment
AnalysisCCPNdata analysis
AnalysisCCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
RefinementMethod: de novo / Software ordinal: 7
Details: de novo protein structure calculation based on chemical shift
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50000 / Conformers submitted total number: 20

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