[English] 日本語
Yorodumi
- PDB-2bug: Solution structure of the TPR domain from Protein phosphatase 5 i... -

+
Open data


ID or keywords:

Loading...

-
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 arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding ...response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / myosin phosphatase activity / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / protein serine/threonine phosphatase activity / mitochondrial transport / 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 / protein-serine/threonine phosphatase / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / regulation of postsynaptic membrane neurotransmitter receptor levels / phosphatase activity / dendritic growth cone / phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / protein dephosphorylation / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / response to lead ion / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Hsp90 protein binding / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus
Similarity search - Function
PPP domain / PP5, C-terminal metallophosphatase 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 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type ...PPP domain / PP5, C-terminal metallophosphatase 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 1 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Sequence detailsG83N MUTATION AND N-TERMINAL HIS TAG

-
Experimental details

-
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.

-
Sample preparation

DetailsContents: 50MM MES, 5MM DTT (PH6.0) 10%D2O, 90% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
155 mM6.0 1.0 atm298.0 K
255 mM6.0 1.0 atm298.0 K
355 mM6.0 1.0 atm298.0 K
455 mM6.0 1.0 atm298.0 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more