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- PDB-8eod: EEVD:Sis1-81 (J domain) bound conformation -

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Basic information

Entry
Database: PDB / ID: 8eod
TitleEEVD:Sis1-81 (J domain) bound conformation
ComponentsProtein SIS1
KeywordsCHAPERONE / J-domain / Sis1 / EEVD
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 / DGSA-distance geometry simulated annealing
AuthorsMatos, C.O. / Pinheiro, G.M.S. / Ramos, C.H.I. / Almeida, F.C.L.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2019/16114-1 Brazil
Sao Paulo Research Foundation (FAPESP)2017/26131-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)313517/2021-5 Brazil
CitationJournal: To Be Published
Title: Structural and dynamical basis for the interaction of HSP70-EEVD with JDP Sis1
Authors: Matos, C.O. / Pinheiro, G.M.S. / Ramos, C.H.I. / Almeida, F.C.L.
History
DepositionOct 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SIS1


Theoretical massNumber of molelcules
Total (without water)11,9001
Polymers11,9001
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein SIS1


Mass: 11900.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SIS1, YNL007C, N2879 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25294

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211isotropic12D 1H-15N HSQC
271isotropic12D 1H-13C HSQC
221isotropic13D HNCO
231isotropic13D HNCA
241isotropic13D HN(CA)CB
251isotropic13D CBCA(CO)NH
281isotropic13D 1H-13C NOESY aliphatic
291isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-13C; U-15N] 15N-13C-Sis11-81:EEVD, 1 mM [U-90% 15N] 15N-Sis11-81:EEVD, 90% H2O/10% D2O
Label: 15N, 13C-Sis11-81 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uM15N-13C-Sis11-81:EEVD[U-13C; U-15N]1
1 mM15N-Sis11-81:EEVD[U-90% 15N]1
Sample conditionsIonic strength: 0.2 M / Ionic strength err: 0.02 / Label: Condition_1 / pH: 7.2 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 900 MHz
Details: spectrometer equipped with an inverse-detection triple resonance z-gradient TXI probe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.refinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.5.2CCPNchemical shift assignment
CcpNmr Analysis2.5.2CCPNpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 4088 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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