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- PDB-7qcy: Two-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, comp... -

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Basic information

Entry
Database: PDB / ID: 7qcy
TitleTwo-state liquid NMR Structure of a PDZ2 Domain from hPTP1E, complexed with RA-GEF2 peptide
ComponentsTyrosine-protein phosphatase non-receptor type 13
KeywordsHYDROLASE / Protein-protein recognition domain
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / fibrillar center / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAshkinadze, D. / Kadavath, H. / Chi, C. / Friedmann, M. / Strotz, D. / Kumari, P. / Minges, M. / Cadalbert, R. / Koenigl, S. / Guentert, P. ...Ashkinadze, D. / Kadavath, H. / Chi, C. / Friedmann, M. / Strotz, D. / Kumari, P. / Minges, M. / Cadalbert, R. / Koenigl, S. / Guentert, P. / Voegeli, B. / Riek, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Atomic resolution protein allostery from the multi-state structure of a PDZ domain.
Authors: Ashkinadze, D. / Kadavath, H. / Pokharna, A. / Chi, C.N. / Friedmann, M. / Strotz, D. / Kumari, P. / Minges, M. / Cadalbert, R. / Konigl, S. / Guntert, P. / Vogeli, B. / Riek, R.
History
DepositionNov 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 13


Theoretical massNumber of molelcules
Total (without water)10,0201
Polymers10,0201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 2000target function
RepresentativeModel #1target function

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 13 / Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / ...Fas-associated protein-tyrosine phosphatase 1 / FAP-1 / PTP-BAS / Protein-tyrosine phosphatase 1E / PTP-E1 / hPTPE1 / Protein-tyrosine phosphatase PTPL1


Mass: 10020.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN13, PNP1, PTP1E, PTPL1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q12923, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D HNCA
131isotropic13D HN(CO)CA
141isotropic13D HN(CA)CB
151isotropic13D HN(COCA)CB
161isotropic12D 1H-13C HSQC
171isotropic12D 1H-15N HSQC
181isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 2 mM [U-100% 13C; U-100% 15N] PDZ2 domain, 2 mM RA-GEF2 peptide, 95% H2O/5% D2O
Label: 15N_13C_PDZ2 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMPDZ2 domain[U-100% 13C; U-100% 15N]1
2 mMRA-GEF2 peptidenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 pD / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 40

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