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- PDB-2bug: Solution structure of the TPR domain from Protein phosphatase 5 i... -

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Basic information

Entry
Database: PDB / ID: 2bug
TitleSolution structure of the TPR domain from Protein phosphatase 5 in complex with Hsp90 derived peptide
Components
  • HSP90
  • SERINE/THREONINE PROTEIN PHOSPHATASE 5
KeywordsHYDROLASE / TETRATRICOPEPTIDE DOMAIN / PROTEIN PHOSPHATASE / HSP90 BINDING / IRON / MANGANESE / METAL-BINDING
Function / homology
Function and homology information


response to arachidonate / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / protein folding chaperone complex / response to morphine / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization ...response to arachidonate / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / protein folding chaperone complex / response to morphine / sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / protein serine/threonine phosphatase activity / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / TPR domain binding / phosphatase activity / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / dendritic growth cone / phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / protein dephosphorylation / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / response to cold / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / Hsp90 protein binding / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane
Similarity search - Function
PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type ...PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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. / TPR repeat 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-alpha / Serine/threonine-protein phosphatase 5 / DSCR1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsCliff, M.J. / Harris, R. / Barford, D. / Ladbury, J.E. / Williams, M.A.
CitationJournal: Structure / Year: 2006
Title: Conformational Diversity in the Tpr Domain-Mediated Interaction of Protein Phosphatase 5 with Hsp90.
Authors: Cliff, M.J. / Harris, R. / Barford, D. / Ladbury, J.E. / Williams, M.A.
History
DepositionJun 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE PROTEIN PHOSPHATASE 5
B: HSP90


Theoretical massNumber of molelcules
Total (without water)16,8592
Polymers16,8592
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)19 / 100LOWEST RESTRAINT ENERGY
RepresentativeModel #4

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Components

#1: Protein SERINE/THREONINE PROTEIN PHOSPHATASE 5 / PROTEIN PHOSPHATASE 5 / PP5 / PPT


Mass: 16211.396 Da / Num. of mol.: 1 / Fragment: TETRATRICOPEPTIDE DOMAIN, RESIDUES 19-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 19-147 WITH N-TERMINAL HIS-TAG / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53041, protein-serine/threonine phosphatase
#2: Protein/peptide HSP90 / DSCR1


Mass: 647.695 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PENTAPEPTIDE, RESIDUES 1-5 / Source method: obtained synthetically / Details: N-TERMINALLY ACETYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9H2A1, UniProt: P07900*PLUS
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 83 TO ASN
Has protein modificationY
Sequence detailsG83N MUTATION AND N-TERMINAL HIS TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HNCO
131CBCA(CO)NH
1411H15N- TOWNY-HSQC
151HNHB
2611H15N- NOESYHSQC
3711H13CNOESYHSQC
481NOESY
491TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DETERMINED FROM 1H13C-NOESYHSQC (13C,15N- LABELLED PROTEIN) AND 1H15N-NOESYHSQC EXPERIMENTS (15N- LABELLED PROTEIN), AND ALSO HYDROGEN ...Text: THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DETERMINED FROM 1H13C-NOESYHSQC (13C,15N- LABELLED PROTEIN) AND 1H15N-NOESYHSQC EXPERIMENTS (15N- LABELLED PROTEIN), AND ALSO HYDROGEN BOND RESTRAINTS FROM HYDROGEN EXCHANGE DATE, ANGLE RESTRAINTS DERIVED FROM CHEMICAL SHIFT DATA BY TALOS.

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Sample preparation

DetailsContents: 50MM MES, 5MM DTT (PH6.0) 10%D2O, 90% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
155 mM61.0 atm298.0 K
255 mM61.0 atm298.0 K
355 mM61.0 atm298.0 K
455 mM61.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
ARIA1.2structure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST RESTRAINT ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 19

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