Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.41 kDa 
• Atom Count: 5556 
• Modelled Residue Count: 658 
• Deposited Residue Count: 702 
• Unique protein chains: 2

4EKK

Akt1 with AMP-PNP

• PDB DOI: 10.2210/pdb4EKK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-04-09 Released: 2012-05-23 
• Deposition Author(s): Wu, W.-I., Vigers, G.P.A., Morales, T.H., Brandhuber, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

An ATP-Site On-Off Switch That Restricts Phosphatase Accessibility of Akt.

Lin, K., Lin, J., Wu, W.I., Ballard, J., Lee, B.B., Gloor, S.L., Vigers, G.P., Morales, T.H., Friedman, L.S., Skelton, N., Brandhuber, B.J.

(2012) Sci Signal 5: ra37-ra37

• PubMed: 22569334 
• DOI: 10.1126/scisignal.2002618
• Primary Citation of Related Structures:  
  4EKK, 4EKL


• PubMed Abstract: 
  

The protein serine-threonine kinase Akt undergoes a substantial conformational change upon activation, which is induced by the phosphorylation of two critical regulatory residues, threonine 308 and serine 473. Paradoxically, treating cells with adenosine 5'-triphosphate (ATP)-competitive inhibitors of Akt results in increased phosphorylation of both residues. We show that binding of ATP-competitive inhibitors stabilized a conformation in which both phosphorylated sites were inaccessible to phosphatases. ATP binding also produced this protection of the phosphorylated sites, whereas interaction with its hydrolysis product adenosine 5'-diphosphate (ADP) or allosteric Akt inhibitors resulted in increased accessibility of these phosphorylated residues. ATP-competitive inhibitors mimicked ATP by targeting active Akt. Forms of Akt activated by an oncogenic mutation or myristoylation were more potently inhibited by the ATP-competitive inhibitors than was wild-type Akt. These data support a new model of kinase regulation, wherein nucleotides modulate an on-off switch in Akt through conformational changes, which is disrupted by ATP-competitive inhibitors.

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Organizational Affiliation: 

Genentech Inc., South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-alpha serine/threonine-protein kinase	A, B	341	Homo sapiens	Mutation(s): 1  Gene Names: AKT1, PKB, RAC EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens) Explore P31749  Go to UniProtKB:  P31749
PHAROS:  P31749 GTEx:  ENSG00000142208

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	C, D	10	Homo sapiens	Mutation(s): 0  Gene Names: GSK3B EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841  Go to UniProtKB:  P49841
PHAROS:  P49841 GTEx:  ENSG00000082701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], H [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN	F [auth A], G [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.637	α = 90
b = 55.853	β = 103.43
c = 91.402	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-09 
• Released Date: 2012-05-23 
Deposition Author(s): Wu, W.-I., Vigers, G.P.A., Morales, T.H., Brandhuber, B.J.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary