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- PDB-1mrv: crystal structure of an inactive Akt2 kinase domain -

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Basic information

Entry
Database: PDB / ID: 1mrv
Titlecrystal structure of an inactive Akt2 kinase domain
ComponentsRAC-beta serine/threonine kinase
KeywordsTRANSFERASE / AGC serine threonine kinase / AKT PKB kinase domain / tumorigenesis / x-ray crystal structure / signal transduction
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 / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / RUNX2 regulates genes involved in cell migration / mammary gland epithelial cell differentiation / RAB GEFs exchange GTP for GDP on RABs / glycogen biosynthetic process / peripheral nervous system myelin maintenance / AKT phosphorylates targets in the cytosol / positive regulation of cell motility / Regulation of TP53 Activity through Association with Co-factors / Co-inhibition by CTLA4 / Constitutive Signaling by AKT1 E17K in Cancer / fat cell differentiation / negative regulation of PERK-mediated unfolded protein response / Regulation of MITF-M-dependent genes involved in pigmentation / Regulation of localization of FOXO transcription factors / CD28 dependent PI3K/Akt signaling / positive regulation of protein targeting to membrane / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / positive regulation of glycogen biosynthetic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / FLT3 Signaling / Downregulation of ERBB2:ERBB3 signaling / regulation of cell migration / molecular function activator activity / VEGFR2 mediated vascular permeability / positive regulation of D-glucose import / protein localization to plasma membrane / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / protein modification process / ruffle membrane / Regulation of PTEN stability and activity / glucose metabolic process / cellular response to insulin stimulus / KEAP1-NFE2L2 pathway / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / insulin receptor signaling pathway / PIP3 activates AKT signaling / cell cortex / early endosome / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / protein stabilization / positive regulation of cell migration / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology 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. ...Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology 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-beta serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, X. / Begley, M. / Morgenstern, K.A. / Gu, Y. / Rose, P. / Zhao, H. / Zhu, X.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of an inactive akt2 kinase domain
Authors: Huang, X. / Begley, M. / Morgenstern, K.A. / Gu, Y. / Rose, P. / Zhao, H. / Zhu, X.
History
DepositionSep 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC-beta serine/threonine kinase


Theoretical massNumber of molelcules
Total (without water)39,3131
Polymers39,3131
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.440, 150.440, 40.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

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Components

#1: Protein RAC-beta serine/threonine kinase / RAC-PK-beta / Protein kinase Akt-2 / Protein kinase B / beta / PKB beta


Mass: 39313.008 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT2
Plasmid details: gene cloned between BamHI & EcoRI, has His6 tag with thrombin cleavage site.
Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31751, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Li2SO4, PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMTris1droppH8.5
3150 mM1dropNaCl
410 %glycerol1drop
514 mMbeta-mercaptoethanol1drop
6100 mMTris1reservoirpH8.5
7200 mM1reservoirLi2SO4
815 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 17360 / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Biso Wilson estimate: 51.93 Å2 / Rsym value: 0.078 / Net I/σ(I): 8.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 11257 / % possible obs: 94.4 % / Num. measured all: 50158 / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PKA in ternary complex

Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 550 -RANDOM
Rwork0.247 ---
all-11922 --
obs-11257 94.4 %-
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 0 74 2148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0093
X-RAY DIFFRACTIONc_angle_deg1.46
Refinement
*PLUS
Rfactor Rfree: 0.307 / Rfactor Rwork: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.43

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