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- PDB-6buu: Crystal structure of AKT1 (aa 144-480) with a bisubstrate -

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Basic information

Entry
Database: PDB / ID: 6buu
TitleCrystal structure of AKT1 (aa 144-480) with a bisubstrate
Components
  • GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
  • RAC-alpha serine/threonine-protein kinase
KeywordsTRANSFERASE / AKT1 / RAC-alpha serine/theronine-protein kinase / kinase / phosphorylated tail / semi-synthesis
Function / homology
Function and homology information


regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / 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 / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels / maternal placenta development / 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 / potassium channel activator activity / establishment of protein localization to mitochondrion / AKT phosphorylates targets in the nucleus / negative regulation of fatty acid beta-oxidation / 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 / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / negative regulation of cilium assembly / cellular response to peptide / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of organ growth / positive regulation of TORC2 signaling / positive regulation of protein localization to centrosome / RUNX2 regulates genes involved in cell migration / interleukin-18-mediated signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / response to fluid shear stress / fibroblast migration / MTOR signalling / positive regulation of cilium assembly / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / response to growth factor / beta-catenin destruction complex / positive regulation of glucose metabolic process / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / cellular response to granulocyte macrophage colony-stimulating factor stimulus / RAB GEFs exchange GTP for GDP on RABs / regulation of microtubule-based process / phosphatidylinositol-3,4-bisphosphate binding / regulation of protein export from nucleus / negative regulation of leukocyte cell-cell adhesion / positive regulation of protein localization to cell surface / peripheral nervous system myelin maintenance / 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 / glycogen biosynthetic process / Maturation of nucleoprotein / cellular response to interleukin-3 / sphingosine-1-phosphate receptor signaling pathway / positive regulation of endodeoxyribonuclease activity / response to growth hormone / regulation of long-term synaptic potentiation / Wnt signalosome / cell migration involved in sprouting angiogenesis / negative regulation of TOR signaling / positive regulation of fibroblast migration / anoikis / protein serine/threonine kinase inhibitor activity / mammalian oogenesis stage / negative regulation of protein localization to nucleus / regulation of postsynapse organization / labyrinthine layer blood vessel development / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / activation-induced cell death of T cells / TORC2 complex binding / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / regulation of myelination / response to food / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / response to UV-A / tau-protein kinase activity
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 / 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
: / RAC-alpha serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
Model detailsMn+bisubstrate
AuthorsChu, N. / Gabelli, S.B. / Cole, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA74305 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA062924 United States
CitationJournal: Cell / Year: 2018
Title: Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis.
Authors: Chu, N. / Salguero, A.L. / Liu, A.Z. / Chen, Z. / Dempsey, D.R. / Ficarro, S.B. / Alexander, W.M. / Marto, J.A. / Li, Y. / Amzel, L.M. / Gabelli, S.B. / Cole, P.A.
History
DepositionDec 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
G: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0547
Polymers81,8484
Non-polymers2063
Water4,288238
1
A: RAC-alpha serine/threonine-protein kinase
F: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0754
Polymers40,9242
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-23 kcal/mol
Surface area15830 Å2
MethodPISA
2
B: RAC-alpha serine/threonine-protein kinase
G: GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9793
Polymers40,9242
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.628, 56.267, 91.837
Angle α, β, γ (deg.)90.000, 105.100, 90.000
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: 39238.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Plasmid: pfastbac
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
Strain (production host): SF9
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Protein/peptide GLY-ARG-PRO-ARG-THR-THR-ZXW-PHE-ALA-GLU


Mass: 1685.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49841*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 238 / 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: 2.68 Å3/Da / Density % sol: 54.18 % / Mosaicity: 1.039 ° / Mosaicity esd: 0.014 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG 3000, 0.1M Hepes HCL, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Oct 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31906 / % possible obs: 94.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Χ2: 2.995 / Net I/σ(I): 17.5 / Num. measured all: 96011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.441.90.13910210.9530.1130.181.35861.9
2.44-2.492.10.13311940.9690.1050.171.41771.4
2.49-2.532.30.13113310.9680.0990.1651.39378.5
2.53-2.592.50.13314740.9620.0970.1661.63688.2
2.59-2.642.80.12616720.9720.0880.1551.5899
2.64-2.730.11216250.9750.0770.1371.81997.7
2.7-2.7730.10816650.9790.0740.1311.94199.9
2.77-2.853.10.10216760.9780.0690.1242.12799
2.85-2.933.10.09416530.9840.0640.1152.30199.5
2.93-3.023.20.08816840.9840.0590.1072.55299.5
3.02-3.133.20.08716900.9850.0580.1052.59499.5
3.13-3.263.30.07816670.9880.0510.0942.99199.5
3.26-3.413.30.07316630.9890.0470.0873.21599.5
3.41-3.583.30.06716830.9910.0430.083.61499.3
3.58-3.813.30.06716850.990.0440.084.10698.9
3.81-4.13.30.06416650.9920.0420.0774.10199
4.1-4.523.30.06216920.9920.0410.0754.56698.9
4.52-5.173.20.06217020.9920.0410.0754.32698.9
5.17-6.513.20.06116990.9910.040.0743.76299.6
6.51-502.90.05317650.9950.0370.0644.22498.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
REFMAC5.8.0135phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4EKK

4ekk


Resolution: 2.4→47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1818 / FOM work R set: 0.839 / SU B: 6.834 / SU ML: 0.162 / SU R Cruickshank DPI: 0.5097 / SU Rfree: 0.2665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1382 4.7 %RANDOM
Rwork0.1831 ---
obs0.1854 28033 86.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.93 Å2 / Biso mean: 37.814 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20.74 Å2
2---1.31 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.4→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 7 238 5743
Biso mean--63.25 33.83 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195687
X-RAY DIFFRACTIONr_bond_other_d0.0020.025347
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.997679
X-RAY DIFFRACTIONr_angle_other_deg1.039312330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9865.015668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42623.309275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2971542
X-RAY DIFFRACTIONr_chiral_restr0.1050.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021346
LS refinement shellResolution: 2.398→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 62 -
Rwork0.21 1341 -
all-1403 -
obs--56.3 %

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