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Yorodumi- PDB-7apj: Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7apj | |||||||||||||||
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Title | Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / kinase / autoinhibition / lipid / membrane / PIP3 / Akt | |||||||||||||||
Function / homology | Function and homology information glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / negative regulation of protein maturation / 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 / negative regulation of lymphocyte migration / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / negative regulation of protein maturation / 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 / negative regulation of lymphocyte migration / 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 / 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 / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of I-kappaB phosphorylation / negative regulation of cilium assembly / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / RUNX2 regulates genes involved in cell migration / positive regulation of organ growth / response to fluid shear stress / cellular response to peptide / negative regulation of endopeptidase activity / interleukin-18-mediated signaling pathway / fibroblast migration / MTOR signalling / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / negative regulation of protein serine/threonine kinase activity / positive regulation of glucose metabolic process / RAB GEFs exchange GTP for GDP on RABs / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of leukocyte cell-cell adhesion / positive regulation of protein localization to cell surface / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of endodeoxyribonuclease activity / peripheral nervous system myelin maintenance / glycogen biosynthetic process / sphingosine-1-phosphate receptor signaling pathway / protein serine/threonine kinase inhibitor activity / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / response to growth hormone / anoikis / AKT phosphorylates targets in the cytosol / response to food / non-canonical NF-kappaB signal transduction / labyrinthine layer blood vessel development / response to UV-A / regulation of myelination / regulation of postsynapse organization / Regulation of TP53 Activity through Association with Co-factors / KSRP (KHSRP) binds and destabilizes mRNA / execution phase of apoptosis / negative regulation of macroautophagy / CTLA4 inhibitory signaling / negative regulation of cGAS/STING signaling pathway / mammalian oogenesis stage / negative regulation of Notch signaling pathway / activation-induced cell death of T cells / regulation of neuron projection development / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / phosphatidylinositol-3,4,5-trisphosphate binding / behavioral response to pain / CD28 dependent PI3K/Akt signaling / apoptotic mitochondrial changes / Regulation of localization of FOXO transcription factors / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of neuron differentiation / positive regulation of glycogen biosynthetic process / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / TOR signaling / positive regulation of fat cell differentiation / positive regulation of G1/S transition of mitotic cell cycle / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / eNOS activation / canonical NF-kappaB signal transduction / Cyclin E associated events during G1/S transition / phosphorylation / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Cyclin A:Cdk2-associated events at S phase entry / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / lipopolysaccharide-mediated signaling pathway / 14-3-3 protein binding / Regulation of TP53 Activity through Acetylation / negative regulation of protein ubiquitination / striated muscle cell differentiation Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Danio rerio (zebrafish) Lama glama (llama) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||||||||
Authors | Truebestein, L. / Hornegger, H. / Leonard, T.A. | |||||||||||||||
Funding support | Austria, 4items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structure of autoinhibited Akt1 reveals mechanism of PIP 3 -mediated activation. Authors: Truebestein, L. / Hornegger, H. / Anrather, D. / Hartl, M. / Fleming, K.D. / Stariha, J.T.B. / Pardon, E. / Steyaert, J. / Burke, J.E. / Leonard, T.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7apj.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7apj.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 7apj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7apj_validation.pdf.gz | 314.9 KB | Display | wwPDB validaton report |
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Full document | 7apj_full_validation.pdf.gz | 320.6 KB | Display | |
Data in XML | 7apj_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 7apj_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/7apj ftp://data.pdbj.org/pub/pdb/validation_reports/ap/7apj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51408.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Danio rerio (zebrafish) Gene: AKT1, PKB, RAC, akt1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P31749, UniProt: M4MD44, non-specific serine/threonine protein kinase |
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#2: Antibody | Mass: 13883.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 200 mM malonate, pH 5.0, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→45.6 Å / Num. obs: 38951 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.18 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.05→2.13 Å / Redundancy: 7.9 % / Num. unique obs: 3750 / CC1/2: 0.658 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UNP, 4EKK, 3EZJ Resolution: 2.05→38.55 Å / SU ML: 0.2714 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9005 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→38.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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