6NPZ

Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis.

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.

(2018) Cell 174: 897-907.e14

  • DOI: 10.1016/j.cell.2018.07.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Akt is a critical protein kinase that drives cancer proliferation, modulates metabolism, and is activated by C-terminal phosphorylation. The current structural model for Akt activation by C-terminal phosphorylation has centered on intramolecular inte ...

    Akt is a critical protein kinase that drives cancer proliferation, modulates metabolism, and is activated by C-terminal phosphorylation. The current structural model for Akt activation by C-terminal phosphorylation has centered on intramolecular interactions between the C-terminal tail and the N lobe of the kinase domain. Here, we employ expressed protein ligation to produce site-specifically phosphorylated forms of purified Akt1 that are well suited for mechanistic analysis. Using biochemical, crystallographic, and cellular approaches, we determine that pSer473-Akt activation is driven by an intramolecular interaction between the C-tail and the pleckstrin homology (PH)-kinase domain linker that relieves PH domain-mediated Akt1 autoinhibition. Moreover, dual phosphorylation at Ser477/Thr479 activates Akt1 through a different allosteric mechanism via an apparent activation loop interaction that reduces autoinhibition by the PH domain and weakens PIP3 affinity. These results provide a new framework for understanding how Akt is controlled in cell signaling and suggest distinct functions for differentially modified Akt forms.


    Organizational Affiliation

    Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. Electronic address: pacole@bwh.harvard.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. Electronic address: gabelli@jhmi.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAC-alpha serine/threonine-protein kinase
A, B
358Homo sapiensMutation(s): 0 
Gene Names: AKT1 (PKB, RAC)
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bisubstrate
F, G
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, F, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
VO4
Query on VO4

Download SDF File 
Download CCD File 
B
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ZXW
Query on ZXW
F, G
NON-POLYMERC15 H24 N7 O14 P3 S

--

SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.321α = 90.00
b = 56.088β = 104.56
c = 92.019γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA74305
National Institutes of Health/National Cancer InstituteUnited StatesCA062924

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release