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- PDB-1o6k: Structure of activated form of PKB kinase domain S474D with GSK3 ... -

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Basic information

Entry
Database: PDB / ID: 1o6k
TitleStructure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
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 / 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 / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / RUNX2 regulates genes involved in cell migration / positive regulation of protein localization to centrosome / mammary gland epithelial cell differentiation / positive regulation of cilium assembly / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / RAB GEFs exchange GTP for GDP on RABs / glycogen biosynthetic process / peripheral nervous system myelin maintenance / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / cellular response to interleukin-3 / Maturation of nucleoprotein / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / regulation of microtubule-based process / negative regulation of protein localization to nucleus / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / positive regulation of cell motility / Regulation of TP53 Activity through Association with Co-factors / regulation of axonogenesis / positive regulation of cell-matrix adhesion / regulation of dendrite morphogenesis / Co-inhibition by CTLA4 / G protein-coupled dopamine receptor signaling pathway / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / establishment of cell polarity / negative regulation of PERK-mediated unfolded protein response / fat cell differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / dynactin binding / Regulation of localization of FOXO transcription factors / epithelial to mesenchymal transition / CD28 dependent PI3K/Akt signaling / Regulation of HSF1-mediated heat shock response / positive regulation of protein targeting to membrane / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / canonical Wnt signaling pathway / positive regulation of glycogen biosynthetic process / NF-kappaB binding / negative regulation of osteoblast differentiation / positive regulation of protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein-containing complex assembly / Cyclin E associated events during G1/S transition / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Cyclin A:Cdk2-associated events at S phase entry / regulation of cellular response to heat / Regulation of TP53 Activity through Acetylation / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / positive regulation of autophagy
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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: 1.7 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)40,8615
Polymers40,2452
Non-polymers6163
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.906, 60.998, 129.410
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 / RAC-PK-BETA / PROTEIN KINASE AKT-2 / PROTEIN KINASE B / BETA / PKB BETA / PROTEIN KINASE BETA / AKT2


Mass: 39121.645 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 146-481 / Mutation: YES
Source method: isolated from a genetically manipulated source
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.: 281 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROTEIN KINASE KNOWN TO PHOSPHORYLATE SEVERAL PROTEINS. ENGINEERED MUTATION IN CHAIN A SER 474 ASP
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: 2.6 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: 10 MG/ML PROTEIN 20 PEG 4K, 10% ISOPROPONAL, 5 MM DTT, pH 7.50
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: ID14-4 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2002
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 116971 / % possible obs: 82.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.3 / % possible all: 63.7
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 27820 / Num. measured all: 116971
Reflection shell
*PLUS
Lowest resolution: 1.79 Å / % possible obs: 63.7 %

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Processing

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

Resolution: 1.7→36.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1566941.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1517 5 %RANDOM
Rwork0.205 ---
obs0.205 30601 76.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.395 Å2 / ksol: 0.337772 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å20 Å2
2---3.02 Å20 Å2
3---7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 33 281 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.122 4 -
obs--0.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROPROTEIN.TOP
X-RAY DIFFRACTION2ANP.PAR
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 3.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0124
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.44

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