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- PDB-5gjj: Glutathionylated hHsp70 SBD -

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Basic information

Entry
Database: PDB / ID: 5gjj
TitleGlutathionylated hHsp70 SBD
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / Hsp70 / SBD / glutathionylation
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / ATP metabolic process / protein folding chaperone / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
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 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGong, W.B. / Yang, J. / Zhang, H. / Perrett, S.
CitationJournal: To Be Published
Title: Structure of glutathionylated hHsp70 SBD (385-641)
Authors: Gong, W.B. / Yang, J. / Zhang, H. / Perrett, S.
History
DepositionJun 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 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 70 kDa protein 1A


Theoretical massNumber of molelcules
Total (without water)27,8571
Polymers27,8571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20810 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 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70.1


Mass: 27857.260 Da / Num. of mol.: 1 / Fragment: UNP residues 385-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
1111isotropic13D HN(CA)CO
1101isotropic13D HBHA(CO)NH
191isotropic13D (H)CCH-TOCSY
181isotropic13D CCH-TOCSY
171isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY aliphatic
1131isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 15N] human Hsp70 SBD (385-641), 10 mM unlabeling sodium phosphate, 5 mM unlabeling DTT, 2 mM unlabeling EDTA, 0.02 % unlabeling DSS, 90% H2O/10% D2O
Label: 15N,13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhuman Hsp70 SBD (385-641)[U-99% 15N]1
10 mMsodium phosphateunlabeling1
5 mMDTTunlabeling1
2 mMEDTAunlabeling1
0.02 %DSSunlabeling1
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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