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- PDB-2lsv: The NMR high resolution structure of yeast Tah1 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 2lsv
TitleThe NMR high resolution structure of yeast Tah1 in complex with the Hsp90 C-terminal tail
Components
  • ATP-dependent molecular chaperone HSP82
  • TPR repeat-containing protein associated with Hsp90
KeywordsCHAPERONE-BINDING PROTEIN/CHAPERONE / CHAPERONE-BINDING PROTEIN-CHAPERONE complex
Function / homology
Function and homology information


The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / R2TP complex / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / R2TP complex / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...: / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / TPR repeat-containing protein associated with Hsp90
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsBack, R. / Dominguez, C. / Rothe, B. / Bobo, C. / Beaufils, C. / Morera, S. / Meyer, P. / Charpentier, B. / Branlant, C. / Allain, F. / Manival, X.
CitationJournal: Structure / Year: 2013
Title: High-Resolution Structural Analysis Shows How Tah1 Tethers Hsp90 to the R2TP Complex.
Authors: Back, R. / Dominguez, C. / Rothe, B. / Bobo, C. / Beaufils, C. / Morera, S. / Meyer, P. / Charpentier, B. / Branlant, C. / Allain, F.H. / Manival, X.
History
DepositionMay 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jun 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 1.4May 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: TPR repeat-containing protein associated with Hsp90
B: ATP-dependent molecular chaperone HSP82


Theoretical massNumber of molelcules
Total (without water)13,4312
Polymers13,4312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein TPR repeat-containing protein associated with Hsp90


Mass: 12392.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TAH1, YCR060W, YCR60W / Plasmid: pKHS / Production host: Escherichia coli (E. coli) / References: UniProt: P25638
#2: Protein/peptide ATP-dependent molecular chaperone HSP82 / 82 kDa heat shock protein / Heat shock protein Hsp90 heat-inducible isoform


Mass: 1038.041 Da / Num. of mol.: 1 / Fragment: C-terminal tail / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02829

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1312D 1H-13C HSQC
1413D H(CCO)NH
1512D F1-filtered, F2-filtered NOESY
1612D 1H-13C HSQC aliphatic
1713D 13C F1-filtered, F3 edited NOESY
1813D 15N F1-filtered, F2 edited NOESY
1922D 1H-13C HSQC aliphatic
11022D 1H-13C HSQC aromatic
11122D F1-filtered, F2-filtered NOESY
11222D 13C F1-filtered, F2-edited NOESY
11323D 13C F1-filtered, F3-edited NOESY aliphatic
11423D 13C F1-filtered, F3-edited NOESY aromatic
11512D 1H-15N HSQC
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11813D 1H-15N NOESY
11912D F1-filterd, F2-filtered TOCSY
12012D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein_1, 1 mM protein_2, 10 mM sodium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] protein_1, 1 mM protein_2, 10 mM sodium phosphate, 150 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
1 mMentity_2-21
10 mMsodium phosphate-31
150 mMsodium chloride-41
1 mMentity_1-5[U-100% 13C; U-100% 15N]2
1 mMentity_2-62
10 mMsodium phosphate-72
150 mMsodium chloride-82
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVIIIBrukerAVIII5001
Bruker AVIIIBrukerAVIII7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2715 / NOE intraresidue total count: 629 / NOE long range total count: 586 / NOE medium range total count: 788 / NOE sequential total count: 712
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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