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- PDB-1p6s: Solution Structure of the Pleckstrin Homology Domain of Human Pro... -

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Basic information

Entry
Database: PDB / ID: 1p6s
TitleSolution Structure of the Pleckstrin Homology Domain of Human Protein Kinase B beta (Pkb/Akt)
ComponentsRAC-beta serine/threonine protein kinase
KeywordsTRANSFERASE / PLECKSTRIN HOMOLOGY DOMAIN / PKB / AKT / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / positive regulation of cap-dependent translational initiation / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / Activation of AKT2 / AKT phosphorylates targets in the nucleus ...retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / positive regulation of cap-dependent translational initiation / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / Activation of AKT2 / AKT phosphorylates targets in the nucleus / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / RUNX2 regulates genes involved in cell migration / mammary gland epithelial cell differentiation / RAB GEFs exchange GTP for GDP on RABs / glycogen biosynthetic process / peripheral nervous system myelin maintenance / AKT phosphorylates targets in the cytosol / positive regulation of cell motility / Regulation of TP53 Activity through Association with Co-factors / Co-inhibition by CTLA4 / Constitutive Signaling by AKT1 E17K in Cancer / fat cell differentiation / negative regulation of PERK-mediated unfolded protein response / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of localization of FOXO transcription factors / CD28 dependent PI3K/Akt signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of protein targeting to membrane / Activation of BAD and translocation to mitochondria / positive regulation of glycogen biosynthetic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Downregulation of ERBB2:ERBB3 signaling / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / FLT3 Signaling / Deactivation of the beta-catenin transactivating complex / regulation of cell migration / molecular function activator activity / VEGFR2 mediated vascular permeability / positive regulation of D-glucose import / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Regulation of PTEN stability and activity / protein modification process / ruffle membrane / cellular response to insulin stimulus / glucose metabolic process / KEAP1-NFE2L2 pathway / Regulation of TP53 Degradation / G beta:gamma signalling through PI3Kgamma / insulin receptor signaling pathway / PIP3 activates AKT signaling / cell cortex / early endosome / non-specific serine/threonine protein kinase / regulation of cell cycle / protein stabilization / intracellular signal transduction / positive regulation of cell migration / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain 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, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
RAC-beta serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsAuguin, D. / Barthe, P. / Auge-Senegas, M.T. / Stern, M.H. / Noguchi, M. / Roumestand, C.
CitationJournal: J.BIOMOL.NMR / Year: 2004
Title: Solution structure and backbone dynamics of the pleckstrin homology domain of the human protein kinase B (PKB/Akt). Interaction with inositol phosphates.
Authors: Auguin, D. / Barthe, P. / Auge-Senegas, M.T. / Stern, M.H. / Noguchi, M. / Roumestand, C.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC-beta serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)13,2331
Polymers13,2331
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)20 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein RAC-beta serine/threonine protein kinase / RAC-PK-beta / Protein kinase Akt-2 / Protein kinase B / beta / PKB beta


Mass: 13233.188 Da / Num. of mol.: 1 / Fragment: Pleckstrin Homology Domain (residues 1-111)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT2 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P31751, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM PKBbeta-PH U-15N,13C; 10mM Tris-HCl; 300mM NaCl; 0.1mM Benzamidine; 0.1mM EDTA; 4mM Inositol-1,4,5-trisphosphate; 90% H2O, 10% D2O90% H2O/10% D2O
20.4mM PKBbeta-PH U-15N; 10mM Tris-HCl; 300mM NaCl; 0.1mM Benzamidine; 0.1mM EDTA; 4mM Inositol-1,4,5-trisphosphate; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.37.4ambient 286 K
20.37.4ambient 286 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.4Ponsprocessing
CINDY1.5Padilladata analysis
XPLOR3.8Brungerstructure solution
XPLOR3.8Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1229 restraints, 1034 are NOE-derived distance constraints, 127 dihedral angle restraints, 68 distance restraints from hydrogen bonds. There are no ...Details: The structures are based on a total of 1229 restraints, 1034 are NOE-derived distance constraints, 127 dihedral angle restraints, 68 distance restraints from hydrogen bonds. There are no constraints for the two peptidic segments: E59-Q61 and R76-T87.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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