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- PDB-2l6j: Tah1 complexed by MEEVD -

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Basic information

Entry
Database: PDB / ID: 2l6j
TitleTah1 complexed by MEEVD
Components
  • C-terminus Hsp90 chaperone peptide MEEVD
  • TPR repeat-containing protein associated with Hsp90
KeywordsPROTEIN BINDING / tetratricopeptide repeat (TPR) / Hsp90 co-factor
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / R2TP complex / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / R2TP complex / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity / positive regulation of protein localization to cell surface / ATP-dependent protein binding / box C/D snoRNP assembly / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / axonal growth cone / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / ESR-mediated signaling / placenta development / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / Chaperone Mediated Autophagy / histone deacetylase binding / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / melanosome / unfolded protein binding / double-stranded RNA binding / protein folding / cellular response to heat / MHC class II protein complex binding / protein-folding chaperone binding / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / 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 ...: / Tetratricopeptide repeat / 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
Heat shock protein HSP 90-beta / TPR repeat-containing protein associated with Hsp90
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsJimenez, B. / Ugwu, F. / Zhao, R. / Orti, L. / Houry, W.A. / Pineda-Lucena, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of minimal tetratricopeptide repeat domain protein Tah1 reveals mechanism of its interaction with Pih1 and Hsp90.
Authors: Jimenez, B. / Ugwu, F. / Zhao, R. / Orti, L. / Makhnevych, T. / Pineda-Lucena, A. / Houry, W.A.
History
DepositionNov 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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: C-terminus Hsp90 chaperone peptide MEEVD


Theoretical massNumber of molelcules
Total (without water)13,1462
Polymers13,1462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 12524.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAH1, TAH1 YCR060W YCR60W, YCR060W, YCR60W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): gold / References: UniProt: P25638
#2: Protein/peptide C-terminus Hsp90 chaperone peptide MEEVD


Mass: 621.657 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P08238*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1332D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D H(CCO)NH
11043D (H)CCH-TOCSY
11113D 1H-15N NOESY
11243D 1H-13C NOESY aliphatic
11312D 15N edited 1H-1H NOESY
11422D 13C-13C COSY
11543D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] Tah1-1, 2 mM Ac-MEEVD-2, 25 mM sodium phosphate-3, 100 mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] Tah1-5, 2 mM Ac-MEEVD-6, 25 mM sodium phosphate-7, 100 mM sodium chloride-8, 90% H2O/10% D2O90% H2O/10% D2O
3800 uM Tah1-9, 1.6 mM Ac-MEEVD-10, 25 mM sodium phosphate-11, 100 mM sodium chloride-12, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-98% 13C; U-98% 15N] Tah1-13, 2 mM Ac-MEEVD-14, 25 mM sodium phosphate-15, 100 mM sodium chloride-16, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTah1-1[U-99% 15N]1
2 mMAc-MEEVD-21
25 mMsodium phosphate-31
100 mMsodium chloride-41
1 mMTah1-5[U-99% 13C; U-99% 15N]2
2 mMAc-MEEVD-62
25 mMsodium phosphate-72
100 mMsodium chloride-82
800 uMTah1-93
1.6 mMAc-MEEVD-103
25 mMsodium phosphate-113
100 mMsodium chloride-123
1 mMTah1-13[U-98% 13C; U-98% 15N]4
2 mMAc-MEEVD-144
25 mMsodium phosphate-154
100 mMsodium chloride-164
Sample conditionsIonic strength: 0.1375 / pH: 8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Prof. W thrich Groupchemical shift assignment
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
UNIO1.0.4Torsten Herrmann Copyright 2002-2010peak picking
UNIO1.0.4Torsten Herrmann Copyright 2002-2010data analysis
UNIO1.0.4Torsten Herrmann Copyright 2002-2010structure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TALOSoriginalCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2051 / NOE intraresidue total count: 359 / NOE long range total count: 510 / NOE medium range total count: 680 / NOE sequential total count: 502
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.304 Å
NMR ensemble rmsDistance rms dev: 0.005 Å / Distance rms dev error: 0.0003 Å

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