4NU1 | pdb_00004nu1

Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide

• PDB DOI: https://doi.org/10.2210/pdb4NU1/pdb

• Classification: TRANSFERASE/PEPTIDE
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-03 Released: 2014-03-26 
• Deposition Author(s): Chu, M.L.-H., Stamos, J.L., Enos, M.D., Shah, N., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.245 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.

Stamos, J.L., Chu, M.L., Enos, M.D., Shah, N., Weis, W.I.

(2014) Elife 3: e01998-e01998

• PubMed: 24642411 
• DOI: https://doi.org/10.7554/eLife.01998
• Primary Citation Related Structures: 
  4NM0, 4NM3, 4NM5, 4NM7, 4NU1


• PubMed Abstract: 
  

  Glycogen synthase kinase-3 (GSK-3) is a key regulator of many cellular signaling pathways. Unlike most kinases, GSK-3 is controlled by inhibition rather than by specific activation. In the insulin and several other signaling pathways, phosphorylation of a serine present in a conserved sequence near the amino terminus of GSK-3 generates an auto-inhibitory peptide. In contrast, Wnt/β-catenin signal transduction requires phosphorylation of Ser/Pro rich sequences present in the Wnt co-receptors LRP5/6, and these motifs inhibit GSK-3 activity. We present crystal structures of GSK-3 bound to its phosphorylated N-terminus and to two of the phosphorylated LRP6 motifs. A conserved loop unique to GSK-3 undergoes a dramatic conformational change that clamps the bound pseudo-substrate peptides, and reveals the mechanism of primed substrate recognition. The structures rationalize target sequence preferences and suggest avenues for the design of inhibitors selective for a subset of pathways regulated by GSK-3. DOI: http://dx.doi.org/10.7554/eLife.01998.001.

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Organizational Affiliation: 
• Department of Structural Biology, Stanford University, Stanford, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 47.8 kDa 
• Atom Count: 3,158 
• Modeled Residue Count: 376 
• Deposited Residue Count: 413 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A	389	Mus musculus	Mutation(s): 0  Gene Names: Gsk3b EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9WV60 (Mus musculus) Explore Q9WV60  Go to UniProtKB:  Q9WV60

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin-1	B	24	Homo sapiens	Mutation(s): 0  Gene Names: AXIN1, AXIN
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens) Explore O15169  Go to UniProtKB:  O15169
PHAROS:  O15169 GTEx:  ENSG00000103126

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AF3	H [auth A]	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
NO3	I [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.245 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.997	α = 90
b = 80.997	β = 90
c = 280.53	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Chu, M.L.-H., Stamos, J.L., Enos, M.D., Shah, N., Weis, W.I.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary