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- PDB-1unr: Crystal structure of the PH domain of PKB alpha in complex with a... -

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Basic information

Entry
Database: PDB / ID: 1unr
TitleCrystal structure of the PH domain of PKB alpha in complex with a sulfate molecule
ComponentsRAC-ALPHA SERINE/THREONINE KINASE
KeywordsTRANSFERASE / PLECKSTRIN HOMOLOGY / PH / PKB / ATK / PHOSPHOINOSITIDE
Function / homology
Function and homology information


regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / mammalian oogenesis stage / regulation of glycogen biosynthetic process / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels ...regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / mammalian oogenesis stage / regulation of glycogen biosynthetic process / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels / cellular response to rapamycin / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / maternal placenta development / establishment of protein localization to mitochondrion / activation-induced cell death of T cells / potassium channel activator activity / AKT phosphorylates targets in the nucleus / negative regulation of fatty acid beta-oxidation / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of glucose metabolic process / cellular response to peptide / positive regulation of TORC2 signaling / RUNX2 regulates genes involved in cell migration / positive regulation of organ growth / interleukin-18-mediated signaling pathway / response to fluid shear stress / fibroblast migration / MTOR signalling / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / response to growth factor / complement receptor mediated signaling pathway / RAB GEFs exchange GTP for GDP on RABs / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / glycogen biosynthetic process / peripheral nervous system myelin maintenance / positive regulation of protein localization to cell surface / sphingosine-1-phosphate receptor signaling pathway / positive regulation of endodeoxyribonuclease activity / phosphorylation / response to growth hormone / cell migration involved in sprouting angiogenesis / anoikis / regulation of postsynapse organization / AKT phosphorylates targets in the cytosol / TORC2 complex binding / positive regulation of fibroblast migration / regulation of myelination / labyrinthine layer blood vessel development / response to UV-A / response to food / Regulation of TP53 Activity through Association with Co-factors / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / KSRP (KHSRP) binds and destabilizes mRNA / execution phase of apoptosis / negative regulation of macroautophagy / Co-inhibition by CTLA4 / negative regulation of cGAS/STING signaling pathway / regulation of neuron projection development / cellular response to stress / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of PERK-mediated unfolded protein response / positive regulation of protein metabolic process / apoptotic mitochondrial changes / phosphatidylinositol-3,4,5-trisphosphate binding / TOR signaling / behavioral response to pain / Regulation of localization of FOXO transcription factors / peptidyl-threonine phosphorylation / protein serine/threonine kinase inhibitor activity / positive regulation of peptidyl-serine phosphorylation / cellular response to vascular endothelial growth factor stimulus / negative regulation of Notch signaling pathway / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / positive regulation of fat cell differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / Mitochondrial unfolded protein response (UPRmt) / positive regulation of glycogen biosynthetic process / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of lipid biosynthetic process / Cyclin E associated events during G1/S transition / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / eNOS activation / T cell costimulation / nitric oxide metabolic process
Similarity search - Function
Protein kinase B alpha, 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 alpha, 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-alpha serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsMilburn, C.C. / Deak, M. / Kelly, S.M. / Price, N.C. / Alessi, D.R. / van Aalten, D.M.F.
Citation
Journal: Biochem. J. / Year: 2003
Title: Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change.
Authors: Milburn, C.C. / Deak, M. / Kelly, S.M. / Price, N.C. / Alessi, D.R. / Van Aalten, D.M.
#1: Journal: Curr.Biol. / Year: 2002
Title: High Resolution Structure of the Pleckstrin Homology Domain of Protein Kinase B/Akt Bound to Phosphatidylinositol (3,4,5)-Trisphosphate
Authors: Milburn, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionSep 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC-ALPHA SERINE/THREONINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8962
Polymers14,8001
Non-polymers961
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.727, 33.963, 42.275
Angle α, β, γ (deg.)90.00, 119.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RAC-ALPHA SERINE/THREONINE KINASE / RAC-PK-ALPHA / PROTEIN KINASE B / PKB / C-AKT


Mass: 14799.705 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.44 Å3/Da / Density % sol: 30 %
Crystal growpH: 8.5 / Details: 0.1 M TRIS (8.5) 0.2 M AMMONIUM SULFATE, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Jan 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.25→15 Å / Num. obs: 27697 / % possible obs: 96.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.5
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.7 / % possible all: 74.6

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1H10

1h10


Resolution: 1.25→20 Å / Num. parameters: 9408 / Num. restraintsaints: 11985 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 902 5 %RANDOM
all0.1714 26794 --
obs0.173 -93 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 767.7 / Occupancy sum non hydrogen: 995.24
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 5 62 1023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0303
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.062
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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