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- PDB-6npz: Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate -

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Basic information

Entry
Database: PDB / ID: 6npz
TitleCrystal structure of Akt1 (aa 123-480) kinase with a bisubstrate
Components
  • RAC-alpha serine/threonine-protein kinase
  • bisubstrate
KeywordsTRANSFERASE / AKT1 / RAC-alpha serine/theronine-protein kinase / kinase / bisubstrate
Function / homology
Function and homology information


positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / mammalian oogenesis stage / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / cellular response to decreased oxygen levels ...positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / mammalian oogenesis stage / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / cellular response to decreased oxygen levels / cellular response to rapamycin / maintenance of protein location in mitochondrion / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / regulation of type B pancreatic cell development / maternal placenta development / positive regulation of anaphase-promoting complex-dependent catabolic process / : / activation-induced cell death of T cells / potassium channel activator activity / AKT phosphorylates targets in the nucleus / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of TORC2 signaling / positive regulation of glucose metabolic process / RUNX2 regulates genes involved in cell migration / beta-arrestin-dependent dopamine receptor signaling pathway / cellular response to peptide / positive regulation of organ growth / mammary gland epithelial cell differentiation / positive regulation of sodium ion transport / interleukin-18-mediated signaling pathway / MTOR signalling / fibroblast migration / response to growth factor / response to fluid shear stress / cellular response to granulocyte macrophage colony-stimulating factor stimulus / RAB GEFs exchange GTP for GDP on RABs / negative regulation of leukocyte cell-cell adhesion / glycogen biosynthetic process / peripheral nervous system myelin maintenance / cell migration involved in sprouting angiogenesis / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of protein localization to cell surface / complement receptor mediated signaling pathway / phosphorylation / sphingosine-1-phosphate receptor signaling pathway / anoikis / sperm glycocalyx / regulation of postsynapse organization / response to growth hormone / AKT phosphorylates targets in the cytosol / positive regulation of fibroblast migration / perinuclear theca / labyrinthine layer blood vessel development / regulation of myelination / Regulation of TP53 Activity through Association with Co-factors / execution phase of apoptosis / TORC2 complex binding / KSRP (KHSRP) binds and destabilizes mRNA / response to UV-A / peptidyl-threonine phosphorylation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Co-inhibition by CTLA4 / negative regulation of macroautophagy / response to food / negative regulation of cGAS/STING signaling pathway / cellular response to stress / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of PERK-mediated unfolded protein response / regulation of neuron projection development / phosphatidylinositol-3,4,5-trisphosphate binding / apoptotic mitochondrial changes / positive regulation of protein metabolic process / behavioral response to pain / TOR signaling / Regulation of localization of FOXO transcription factors / cellular response to vascular endothelial growth factor stimulus / CD28 dependent PI3K/Akt signaling / positive regulation of peptidyl-serine phosphorylation / negative regulation of Notch signaling pathway / Activation of BAD and translocation to mitochondria / positive regulation of blood vessel endothelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of glycogen biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine kinase inhibitor activity / Mitochondrial unfolded protein response (UPRmt) / positive regulation of fat cell differentiation / response to insulin-like growth factor stimulus / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of lipid biosynthetic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Cyclin E associated events during G1/S transition / vascular endothelial cell response to laminar fluid shear stress
Similarity search - Function
Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / PH domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. ...Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / PH domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
: / TRIETHYLENE GLYCOL / VANADATE ION / RAC-alpha serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.12 Å
Model detailsMn+bisubstrate
AuthorsChu, N. / Cole, P.A. / Gabelli, S.B.
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
DepositionJan 18, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionJan 30, 2019ID: 6C0I
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 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 2.1Oct 16, 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: bisubstrate
G: bisubstrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,88612
Polymers86,1594
Non-polymers7278
Water8,557475
1
A: RAC-alpha serine/threonine-protein kinase
F: bisubstrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4906
Polymers43,0792
Non-polymers4104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-10 kcal/mol
Surface area15500 Å2
MethodPISA
2
B: RAC-alpha serine/threonine-protein kinase
G: bisubstrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3966
Polymers43,0792
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-15 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.321, 56.088, 92.019
Angle α, β, γ (deg.)90.000, 104.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABFG

#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: 41393.801 Da / Num. of mol.: 2 / Fragment: UNP residues 123-480
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 bisubstrate


Mass: 1685.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 5 types, 483 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.99958 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99958 Å / Relative weight: 1
ReflectionResolution: 2.12→29.82 Å / Num. obs: 48316 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 10.2 / Num. measured all: 326363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.12-2.186.60.72133320.8380.2970.78283.5
8.97-29.826.90.076800.9960.0290.07697.5

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 6BUU

6buu


Resolution: 2.12→29.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.353 / SU ML: 0.141 / SU R Cruickshank DPI: 0.2126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.19
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2364 4.9 %RANDOM
Rwork0.1853 ---
obs0.1881 45932 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 168.16 Å2 / Biso mean: 39.787 Å2 / Biso min: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å21.28 Å2
2---0.72 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 2.12→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 35 475 6024
Biso mean--63.57 45.77 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135725
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175303
X-RAY DIFFRACTIONr_angle_refined_deg2.061.6777715
X-RAY DIFFRACTIONr_angle_other_deg1.5171.5912296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45421.429315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.329151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9241542
X-RAY DIFFRACTIONr_chiral_restr0.1030.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026245
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021284
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 157 -
Rwork0.249 3066 -
all-3223 -
obs--90.1 %

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