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- PDB-1o6l: Crystal structure of an activated Akt/protein kinase B (PKB-PIF c... -

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Basic information

Entry
Database: PDB / ID: 1o6l
TitleCrystal structure of an activated Akt/protein kinase B (PKB-PIF chimera) ternary complex with AMP-PNP and GSK3 peptide
Components
  • GLYCOGEN SYNTHASE KINASE-3 BETA
  • RAC-BETA SERINE/THREONINE PROTEIN KINASE
KeywordsTRANSFERASE / PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE
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 / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / regulation of microtubule anchoring at centrosome ...retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / neuron projection organization / negative regulation of type B pancreatic cell development / superior temporal gyrus development / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / RUNX2 regulates genes involved in cell migration / negative regulation of dopaminergic neuron differentiation / positive regulation of protein localization to centrosome / maintenance of cell polarity / positive regulation of fatty acid beta-oxidation / mammary gland epithelial cell differentiation / positive regulation of cilium assembly / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation of glucose metabolic process / beta-catenin destruction complex / tau-protein kinase / RAB GEFs exchange GTP for GDP on RABs / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / peripheral nervous system myelin maintenance / glycogen biosynthetic process / Maturation of nucleoprotein / cellular response to interleukin-3 / negative regulation of TOR signaling / Wnt signalosome / positive regulation of cell motility / negative regulation of protein localization to nucleus / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of epithelial to mesenchymal transition / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / Regulation of TP53 Activity through Association with Co-factors / G protein-coupled dopamine receptor signaling pathway / CTLA4 inhibitory signaling / regulation of axonogenesis / regulation of dendrite morphogenesis / tau-protein kinase activity / establishment of cell polarity / glycogen metabolic process / ER overload response / regulation of neuron projection development / fat cell differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / dynactin binding / Regulation of localization of FOXO transcription factors / NF-kappaB binding / epithelial to mesenchymal transition / positive regulation of glycogen biosynthetic process / positive regulation of protein targeting to membrane / Activation of BAD and translocation to mitochondria / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / canonical Wnt signaling pathway / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Cyclin E associated events during G1/S transition / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Cyclin A:Cdk2-associated events at S phase entry / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation
Similarity search - Function
Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / : / Glycogen synthase kinase 3, catalytic domain / Protein kinase, C-terminal / Protein kinase C terminal domain / 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 / : / Glycogen synthase kinase 3, catalytic domain / Protein kinase, C-terminal / Protein kinase C terminal domain / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / RAC-beta serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYang, J. / Cron, P. / Good, V.M. / Thompson, V. / Hemmings, B.A. / Barford, D.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Crystal Structure of an Activated Akt/Protein Kinase B Ternary Complex with Gsk-3 Peptide and AMP-Pnp
Authors: Yang, J. / Cron, P. / Good, V.M. / Thompson, V. / Hemmings, B.A. / Barford, D.
History
DepositionOct 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAC-BETA SERINE/THREONINE PROTEIN KINASE
C: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1285
Polymers40,5122
Non-polymers6163
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.936, 60.997, 131.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCHAIN A IS A MONOMER, BUT THIS ENTRY IS CLASSIFIEDAS A DIMER AS CHAIN A IS IN COMPLEX WITH A PEPTIDE(CHAIN C), FORMING A DIMERIC ASSOCIATION.

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Components

#1: Protein RAC-BETA SERINE/THREONINE PROTEIN KINASE / PROTEIN KINASE AKT-2 / PROTEIN KINASE B BETA RAC-PK-BETA / PKB BETA


Mass: 39388.855 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 146 - 467 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PKBBETA RESIDUES 146-467 FUSED TO EEQEMFEDFDYIADW / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P31751, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide GLYCOGEN SYNTHASE KINASE-3 BETA / GSK-3 BETA


Mass: 1123.220 Da / Num. of mol.: 1 / Fragment: PEPTIDE, RESIDUES 3-12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P49841, EC: 2.7.1.37
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPKBBETA RESIDUES 146-467 FUSED TO EEQEMFEDFDYIADW

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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: 2.6 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: 10 MG/ML PROTEIN, 20% (W/V) POLYETHYLENE, GLYCOL 4000, 10% (V/V) ISOPROPANOL, 0.1 M HEPES (PH 7.5), 5 MM DTT
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25 mMAMP-PNP-MnCl21drop
30.6 mMGSK3beta-peptide1drop
420 %(w/v)PEG40001reservoir
510 %(v/v)iso-propanol1reservoir
60.1 MHEPES1reservoirpH7.5
75 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. obs: 150113 / % possible obs: 94.2 % / Redundancy: 3.51 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 6.1
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.4 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. obs: 42775 / Num. measured all: 150113
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CDK1

Resolution: 1.6→37.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1547408.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 450-466 WERE NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2132 5 %RANDOM
Rwork0.198 ---
obs0.198 42519 87.5 %-
Solvent computationSolvent model: FLAT MODE / Bsol: 17.3128 Å2 / ksol: 0.308674 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.19 Å20 Å20 Å2
2---3.74 Å20 Å2
3---8.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 33 415 3118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 218 5.1 %
Rwork0.264 4048 -
obs--53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ANP.PAR
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 4.4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0122
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.51

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