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- PDB-5xir: Solution structure for human HSP70 substrate binding domain L542Y... -

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Basic information

Entry
Database: PDB / ID: 5xir
TitleSolution structure for human HSP70 substrate binding domain L542Y mutant
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / heat shock protein 70 kDa / apo state
Function / homology
Function and homology information


: / negative regulation of inclusion body assembly / cellular heat acclimation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...: / negative regulation of inclusion body assembly / cellular heat acclimation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / aggresome / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / Dengue Virus Genome Translation and Replication / cellular response to unfolded protein / regulation of protein ubiquitination / HSF1-dependent transactivation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / transcription regulator inhibitor activity / ATP metabolic process / endoplasmic reticulum unfolded protein response / heat shock protein binding / positive regulation of erythrocyte differentiation / negative regulation of protein ubiquitination / centriole / protein folding chaperone / inclusion body / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of RNA splicing / positive regulation of interleukin-8 production / negative regulation of transforming growth factor beta receptor signaling pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of cell growth / PKR-mediated signaling / G protein-coupled receptor binding / histone deacetylase binding / disordered domain specific binding / : / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / protein refolding / virus receptor activity / cellular response to oxidative stress / blood microparticle / vesicle / ficolin-1-rich granule lumen / positive regulation of canonical NF-kappaB signal transduction / nuclear speck / protein stabilization / cadherin binding / negative regulation of cell population proliferation / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / focal adhesion / centrosome / positive regulation of gene expression / ubiquitin protein ligase binding / Neutrophil degranulation / 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 / : / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHoshikawa, M. / Tochio, N. / Tate, S.
CitationJournal: Molecules / Year: 2018
Title: Substrate Binding Switches the Conformation at the Lynchpin Site in the Substrate-Binding Domain of Human Hsp70 to Enable Allosteric Interdomain Communication.
Authors: Umehara, K. / Hoshikawa, M. / Tochio, N. / Tate, S.I.
History
DepositionApr 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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 70 kDa protein 1A


Theoretical massNumber of molelcules
Total (without water)20,3741
Polymers20,3741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 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: 20373.900 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 381-564 / Mutation: L542Y
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
111isotropic13D HNCO
121isotropic13D HN(CA)CO
131isotropic13D HN(CO)CA
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
1101isotropic13D HN(CA)CB
191isotropic13D C(CO)NH
181isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic13D CCH-TOCSY
1111isotropic13D (H)CCH-COSY
1151isotropic11H-15N NOESY
1141isotropic13D 1H-13C NOESY
1131isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 50 mM potassium phosphate, 50 mM potassium chloride, 10 mM DTT, 94% H2O/6% D2O
Label: L542Y / Solvent system: 94% H2O/6% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
10 mMDTTnatural abundance1
Sample conditionsIonic strength: 100 M / Label: condition1 / pH: 7 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGROKobayashi, N.data analysis
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
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: 10

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