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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 5Serine/threonine-specific protein kinase
KeywordsHYDROLASE / TETRATRICOPEPTIDE DOMAIN / PROTEIN PHOSPHATASE / HSP90 BINDING / IRON / MANGANESE / METAL-BINDING
Function / homology
Function and homology information


Signaling by ERBB2 / Regulation of PLK1 Activity at G2/M Transition / eNOS activation / Regulation of actin dynamics for phagocytic cup formation / vRNP Assembly / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Scavenging by Class F Receptors / HSP90 chaperone cycle for steroid hormone receptors (SHR) / HSF1 activation ...Signaling by ERBB2 / Regulation of PLK1 Activity at G2/M Transition / eNOS activation / Regulation of actin dynamics for phagocytic cup formation / vRNP Assembly / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Scavenging by Class F Receptors / HSP90 chaperone cycle for steroid hormone receptors (SHR) / HSF1 activation / Anchoring of the basal body to the plasma membrane / Chaperone Mediated Autophagy / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / ESR-mediated signaling / Downregulation of ERBB2 signaling / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Neutrophil degranulation / Interleukin-4 and Interleukin-13 signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Negative regulation of MAPK pathway / Attenuation phase / Constitutive Signaling by EGFRvIII / PIWI-interacting RNA (piRNA) biogenesis / Recruitment of mitotic centrosome proteins and complexes / VEGFR2 mediated vascular permeability / VEGFA-VEGFR2 Pathway / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / Uptake and function of diphtheria toxin / Loss of Nlp from mitotic centrosomes / Recruitment of NuMA to mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / response to arachidonic acid / histone dephosphorylation / proximal dendrite / positive regulation of glucocorticoid receptor signaling pathway / peptidyl-threonine dephosphorylation / peptidyl-serine dephosphorylation / chaperone complex / protein-serine/threonine phosphatase / positive regulation of protein polymerization / protein insertion into mitochondrial outer membrane / G-protein alpha-subunit binding / protein serine/threonine phosphatase activity / telomerase holoenzyme complex assembly / response to morphine / mitochondrial transport / chaperone-mediated autophagy / positive regulation of cellular protein catabolic process / central nervous system neuron axonogenesis / TPR domain binding / phosphatase activity / dendritic growth cone / phosphoprotein phosphatase activity / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / axon extension / protein unfolding / regulation of protein ubiquitination / DNA polymerase binding / regulation of protein complex assembly / regulation of cellular protein localization / cofactor metabolic process / positive regulation of tau-protein kinase activity / MHC class II protein complex binding / GTPase binding / protein tyrosine kinase binding / axonal growth cone / ADP binding / endocytic vesicle lumen / establishment of cell polarity / ciliary basal body-plasma membrane docking / response to unfolded protein / protein folding chaperone / protein heterooligomerization / regulation of nitric-oxide synthase activity / negative regulation of protein phosphorylation / response to cold / lysosomal lumen / positive regulation of telomerase activity / ATPase activity, coupled / nitric-oxide synthase regulator activity / negative regulation of neuron death / Hsp90 protein binding / protein dephosphorylation / ERBB2 signaling pathway / tau protein binding / cellular response to cadmium ion / regulation of cellular response to heat / response to lead ion / cellular response to hydrogen peroxide / melanosome / histone deacetylase binding / vascular endothelial growth factor receptor signaling pathway / regulation of G2/M transition of mitotic cell cycle / receptor-mediated endocytosis / Fc-gamma receptor signaling pathway involved in phagocytosis / protein refolding
Tetratricopeptide repeat / Histidine kinase/HSP90-like ATPase / Calcineurin-like phosphoesterase domain, ApaH type / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Serine/threonine protein phosphatase 5 / Tetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat-containing domain / PPP domain / TPR repeat region circular profile. / Heat shock protein Hsp90, conserved site ...Tetratricopeptide repeat / Histidine kinase/HSP90-like ATPase / Calcineurin-like phosphoesterase domain, ApaH type / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Serine/threonine protein phosphatase 5 / Tetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat-containing domain / PPP domain / TPR repeat region circular profile. / Heat shock protein Hsp90, conserved site / TPR repeat profile. / Heat shock hsp90 proteins family signature. / Serine/threonine specific protein phosphatases signature. / PPP5 TPR repeat region / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Tetratricopeptide repeat / Hsp90 protein / Calcineurin-like phosphoesterase / PP5, C-terminal metallophosphatase domain / HSP90, C-terminal domain / Histidine kinase/HSP90-like ATPase superfamily / Metallo-dependent phosphatase-like / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90 family / Tetratricopeptide repeat 1
Heat shock protein HSP 90-alpha / Serine/threonine-protein phosphatase 5 / DSCR1
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.
Validation Report
SummaryFull reportAbout validation report
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

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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
Water0
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/peptide SERINE/THREONINE PROTEIN PHOSPHATASE 5 / Serine/threonine-specific protein kinase / PROTEIN PHOSPHATASE 5 / PP5 / PPT


Mass: 16211.396 Da / Num. of mol.: 1 / Details: RESIDUES 19-147 WITH N-TERMINAL HIS-TAG / Fragment: TETRATRICOPEPTIDE DOMAIN, RESIDUES 19-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
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 / Details: N-TERMINALLY ACETYLATED / Fragment: C-TERMINAL PENTAPEPTIDE, RESIDUES 1-5 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9H2A1, UniProt: P07900*PLUS
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 83 TO ASN
Sequence detailsG83N MUTATION AND N-TERMINAL HIS TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Solution-ID: 1

Conditions-IDExperiment-IDType
11HNCA
12HNCO
13CBCA(CO)NH
141H15N- TOWNY-HSQC
15HNHB
261H15N- NOESYHSQC
371H13CNOESYHSQC
48NOESY
49TOCSY
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 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

Ionic strength: 55 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

Conditions-ID
1
2
3
4

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NMR measurement

NMR spectrometer

Manufacturer: Varian / Model: INOVA / Type: Varian INOVA

Field strength (MHz)Spectrometer-ID
5001
8002
8003
6004

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Processing

NMR software

Name: ARIA / Version: 1.2

DeveloperClassification
BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
structure 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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