[English] 日本語
Yorodumi
- PDB-2kyl: Solution structure of MAST2-PDZ complexed with the C-terminus of PTEN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kyl
TitleSolution structure of MAST2-PDZ complexed with the C-terminus of PTEN
Components
  • C-terminus of Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
  • Microtubule-associated serine/threonine-protein kinase 2
KeywordsTRANSFERASE / PDZ / complex / kinase
Function / homology
Function and homology information


inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / negative regulation of dendritic spine morphogenesis / spermatid differentiation / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / negative regulation of epithelial to mesenchymal transition / phosphatidylinositol dephosphorylation / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / brain morphogenesis / regulation of interleukin-12 production / myosin phosphatase activity / protein serine/threonine phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / molecular function inhibitor activity / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / negative regulation of vascular associated smooth muscle cell proliferation / social behavior / negative regulation of cellular senescence / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / Synthesis of PIPs at the plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / multicellular organismal response to stress / phosphatase binding / localization / prepulse inhibition / negative regulation of peptidyl-serine phosphorylation / cytoskeleton organization / synapse assembly / Regulation of PTEN localization / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration / locomotory behavior / negative regulation of protein phosphorylation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / central nervous system development / protein tyrosine phosphatase activity / cell projection / PDZ domain binding / cell motility / TP53 Regulates Metabolic Genes / regulation of protein stability / cytoplasmic side of plasma membrane / PML body / Regulation of PTEN stability and activity / positive regulation of DNA-binding transcription factor activity / microtubule cytoskeleton / cell migration / Ovarian tumor domain proteases / negative regulation of neuron projection development / Downstream TCR signaling / heart development / microtubule binding / dendritic spine / postsynaptic density / learning or memory
Similarity search - Function
Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / PTEN, phosphatase domain / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein ...Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / PTEN, phosphatase domain / Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / Inositol hexakisphosphate / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / C2 domain superfamily / Protein-tyrosine phosphatase-like / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Microtubule-associated serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTerrien, E. / Wolff, N. / Cordier, F. / Simenel, C. / Lafon, M. / Delepierre, M.
CitationJournal: To be Published
Title: Solution structure of MAST2-PDZ complexed with the C-terminus of PTEN
Authors: Terrien, E. / Wolff, N. / Cordier, F. / Simenel, C. / Lafon, M. / Prehaud, C. / Delepierre, M.
History
DepositionJun 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated serine/threonine-protein kinase 2
B: C-terminus of Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN


Theoretical massNumber of molelcules
Total (without water)12,0122
Polymers12,0122
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Microtubule-associated serine/threonine-protein kinase 2


Mass: 10451.940 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P0Q8, non-specific serine/threonine protein kinase
#2: Protein/peptide C-terminus of Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / C-terminus of PTEN


Mass: 1559.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P60484

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D HNCA
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D HN(COCA)CB
11313D 13C-selected/12C,14N-selected NOESY
11413D 15N-selected/12C,14N-selected NOESY

-
Sample preparation

DetailsContents: 0.6mM [U-100% 13C; U-100% 15N] PDZ-domain-1, 1.2mM PTEN-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMPDZ-domain-1[U-100% 13C; U-100% 15N]1
1.2 mMPTEN-21
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
VnmrJVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1317 / NOE intraresidue total count: 570 / NOE long range total count: 270 / NOE medium range total count: 155 / NOE sequential total count: 244
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum upper distance constraint violation: 0.38 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0524 Å / Distance rms dev error: 0.0005 Å

+
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://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