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- PDB-4ekk: Akt1 with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4ekk
TitleAkt1 with AMP-PNP
Components
  • Glycogen synthase kinase-3 beta
  • RAC-alpha serine/threonine-protein kinase
KeywordsTRANSFERASE / Phosphotransferase
Function / homology
Function and homology information


glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / regulation of type B pancreatic cell development ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / maternal placenta development / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / establishment of protein localization to mitochondrion / negative regulation of fatty acid beta-oxidation / regulation of glycogen biosynthetic process / AKT phosphorylates targets in the nucleus / regulation of microtubule anchoring at centrosome / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of glycogen (starch) synthase activity / neuron projection organization / beta-catenin destruction complex disassembly / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / negative regulation of cilium assembly / positive regulation of I-kappaB phosphorylation / superior temporal gyrus development / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of protein localization to cilium / : / negative regulation of glycogen biosynthetic process / response to fluid shear stress / RUNX2 regulates genes involved in cell migration / negative regulation of dopaminergic neuron differentiation / positive regulation of organ growth / cellular response to peptide / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fibroblast migration / interleukin-18-mediated signaling pathway / MTOR signalling / positive regulation of sodium ion transport / positive regulation of cilium assembly / mammary gland epithelial cell differentiation / negative regulation of endopeptidase activity / negative regulation of protein acetylation / negative regulation of protein serine/threonine kinase activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of protein export from nucleus / positive regulation of protein localization to cell surface / positive regulation of endodeoxyribonuclease activity / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / 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 / Maturation of nucleoprotein / protein serine/threonine kinase inhibitor activity / sphingosine-1-phosphate receptor signaling pathway / cellular response to interleukin-3 / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / Wnt signalosome / negative regulation of TOR signaling / response to growth hormone / negative regulation of protein localization to nucleus / anoikis / glycogen biosynthetic process / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of long-term synaptic potentiation / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / labyrinthine layer blood vessel development / response to food / response to UV-A / negative regulation of calcineurin-NFAT signaling cascade / non-canonical NF-kappaB signal transduction / positive regulation of cell-matrix adhesion / regulation of myelination / regulation of axon extension / regulation of postsynapse organization / KSRP (KHSRP) binds and destabilizes mRNA / G protein-coupled dopamine receptor signaling pathway
Similarity search - Function
Protein kinase B alpha, 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 alpha, 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-alpha serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, W.-I. / Vigers, G.P.A. / Morales, T.H. / Brandhuber, B.J.
CitationJournal: Sci.Signal. / Year: 2012
Title: An ATP-Site On-Off Switch That Restricts Phosphatase Accessibility of Akt.
Authors: Lin, K. / Lin, J. / Wu, W.I. / Ballard, J. / Lee, B.B. / Gloor, S.L. / Vigers, G.P. / Morales, T.H. / Friedman, L.S. / Skelton, N. / Brandhuber, B.J.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAC-alpha serine/threonine-protein kinase
B: RAC-alpha serine/threonine-protein kinase
C: Glycogen synthase kinase-3 beta
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,41310
Polymers81,1804
Non-polymers1,2326
Water1,802100
1
A: RAC-alpha serine/threonine-protein kinase
C: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2065
Polymers40,5902
Non-polymers6163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-17 kcal/mol
Surface area15230 Å2
MethodPISA
2
B: RAC-alpha serine/threonine-protein kinase
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2065
Polymers40,5902
Non-polymers6163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-18 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.637, 55.853, 91.402
Angle α, β, γ (deg.)90.00, 103.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RAC-alpha serine/threonine-protein kinase / Protein kinase B / PKB / Protein kinase B alpha / PKB alpha / Proto-oncogene c-Akt / RAC-PK-alpha


Mass: 39466.969 Da / Num. of mol.: 2 / Fragment: UNP residues 144-480 / Mutation: S473D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Protein/peptide Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 1123.220 Da / Num. of mol.: 2 / Fragment: UNP residues 3-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLY TO SER CONFLICT IN UNP ENTRY P31749

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 20% PEG4K, 100mM Tris-pH7.5, Under Oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2003 / Details: Confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 21267 / Num. obs: 21128 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Rsym value: 0.16 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.32 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.69 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.847 / SU B: 15.603 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27998 1084 5.1 %RANDOM
Rwork0.217 ---
obs0.2202 20035 100 %-
all-21267 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.86 Å2
2---0.3 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 66 100 5556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9817522
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43123.285274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.384151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7291542
X-RAY DIFFRACTIONr_chiral_restr0.0720.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214234
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3661.53264
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69625248
X-RAY DIFFRACTIONr_scbond_it0.80932318
X-RAY DIFFRACTIONr_scangle_it1.4244.52274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 74 -
Rwork0.294 1347 -
obs--100 %

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