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- PDB-5z8q: Solution structure of the SBDalpha domain of yeast Ssa1 -

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Basic information

Entry
Database: PDB / ID: 5z8q
TitleSolution structure of the SBDalpha domain of yeast Ssa1
ComponentsHeat shock protein SSA1Heat shock response
KeywordsCHAPERONE / yeast Ssa1 / SBDalpha domain
Function / homology
Function and homology information


: / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / fungal-type cell wall / response to oxygen levels / clathrin coat disassembly / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / fungal-type vacuole membrane ...: / Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitochondria-associated ubiquitin-dependent protein catabolic process / fungal-type cell wall / response to oxygen levels / clathrin coat disassembly / SRP-dependent cotranslational protein targeting to membrane, translocation / protein targeting to mitochondrion / fungal-type vacuole membrane / stress granule disassembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / transcription repressor complex / ATP-dependent protein folding chaperone / protein polyubiquitination / protein import into nucleus / unfolded protein binding / protein folding / cytoplasmic translation / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / tRNA binding / negative regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, nucleotide binding domain / Up-down Bundle / Mainly Alpha
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. / 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
DepositionFeb 1, 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: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model

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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)10,7891
Polymers10,7891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6410 Å2
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 response / Heat shock protein YG100


Mass: 10788.742 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
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
1141isotropic13D HNCO
1131isotropic13D HN(CA)CO
1121isotropic13D C(CO)NH
1111isotropic13D HBHA(CO)NH
1101isotropic13D (H)CCH-TOCSY
191isotropic13D CCH-TOCSY
181isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] Ssa1 SBDalpha, 90% H2O/10% D2O
Label: 15N/13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: Ssa1 SBDalpha / 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: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / 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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