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- PDB-5z8i: Solution structure of the SBDbeta domain of yeast Ssa1 -

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Basic information

Entry
Database: PDB / ID: 5z8i
TitleSolution structure of the SBDbeta domain of yeast Ssa1
ComponentsHeat shock protein SSA1
KeywordsCHAPERONE / Hsp70 / SBDbeta
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / mitochondria-associated ubiquitin-dependent protein catabolic process / clathrin coat disassembly / fungal-type cell wall / response to oxygen levels / Regulation of HSF1-mediated heat shock response / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / stress granule disassembly ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / mitochondria-associated ubiquitin-dependent protein catabolic process / clathrin coat disassembly / fungal-type cell wall / response to oxygen levels / Regulation of HSF1-mediated heat shock response / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / stress granule disassembly / fungal-type vacuole membrane / chaperone cofactor-dependent protein refolding / protein folding chaperone / Neutrophil degranulation / heat shock protein binding / transcription repressor complex / ATP-dependent protein folding chaperone / protein polyubiquitination / protein import into nucleus / unfolded protein binding / protein folding / cellular response to heat / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasmic translation / tRNA binding / negative regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Heat shock protein SSA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsGong, W. / Hu, W. / Wu, H. / Perrett, S.
Funding support China, 8items
OrganizationGrant numberCountry
the National Key R&D Program of China2017YFA0504000 China
the National Natural Science Foundation of China31570780 China
the National Natural Science Foundation of China31200578 China
the National Natural Science Foundation of China31470747 China
the National Natural Science Foundation of China31770829 China
the National Natural Science Foundation of China31300631 China
the National Natural Science Foundation of China21673278 China
the Beijing Natural Science Foundation5172026 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The C-terminal GGAP motif of Hsp70 mediates substrate recognition and stress response in yeast.
Authors: Gong, W. / Hu, W. / Xu, L. / Wu, H. / Wu, S. / Zhang, H. / Wang, J. / Jones, G.W. / Perrett, S.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
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: Heat shock protein SSA1


Theoretical massNumber of molelcules
Total (without water)18,7741
Polymers18,7741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Heat shock protein SSA1 / Heat shock protein YG100


Mass: 18774.189 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: SSA1, YAL005C / Production host: Escherichia coli (E. coli) / References: UniProt: P10591

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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 CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HNCO
161isotropic13D HN(CA)CO
1101isotropic13D C(CO)NH
191isotropic13D HBHA(CO)NH
181isotropic13D CCH-TOCSY
171isotropic13D (H)CCH-TOCSY
1111isotropic13D 15N-edited NOESY
1121isotropic13D 13C-edited NOESY
1131isotropic13D 13C-edited aromatic NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-13C; U-15N] Ssa1, 90% H2O/10% D2O / Label: 15N/13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Ssa1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20 mM NaH2PO4/Na2HPO4, 50 mM NaCl, 1 mM DTT, 1 mM EDTA
Ionic strength: 90 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian DD2 / Manufacturer: Varian / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
Refinement
MethodSoftware ordinal
torsion angle dynamics1
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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