8VMG

Crystal structure of GSK-3 26-383 bound to Axin 383-435


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3 beta.

Enos, M.D.Gavagan, M.Jameson, N.Zalatan, J.G.Weis, W.I.

(2024) Sci Signal 17

  • DOI: https://doi.org/10.1126/scisignal.ado0881
  • Primary Citation of Related Structures:  
    8VME, 8VMF, 8VMG

  • PubMed Abstract: 

    Glycogen synthase kinase 3β (GSK-3β) targets specific signaling pathways in response to distinct upstream signals. We used structural and functional studies to dissect how an upstream phosphorylation step primes the Wnt signaling component β-catenin for phosphorylation by GSK-3β and how scaffolding interactions contribute to this reaction. Our crystal structure of GSK-3β bound to a phosphoprimed β-catenin peptide confirmed the expected binding mode of the phosphoprimed residue adjacent to the catalytic site. An aspartate phosphomimic in the priming site of β-catenin adopted an indistinguishable structure but reacted approximately 1000-fold slower than the native phosphoprimed substrate. This result suggests that substrate positioning alone is not sufficient for catalysis and that native phosphopriming interactions are necessary. We also obtained a structure of GSK-3β with an extended peptide from the scaffold protein Axin that bound with greater affinity than that of previously crystallized Axin fragments. This structure neither revealed additional contacts that produce the higher affinity nor explained how substrate interactions in the GSK-3β active site are modulated by remote Axin binding. Together, our findings suggest that phosphopriming and scaffolding produce small conformational changes or allosteric effects, not captured in the crystal structures, that activate GSK-3β and facilitate β-catenin phosphorylation. These results highlight limitations in our ability to predict catalytic activity from structure and have potential implications for the role of natural phosphomimic mutations in kinase regulation and phosphosite evolution.


  • Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94035, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
364Mus musculusMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WV60
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Axin-1
C, D
60Homo sapiensMutation(s): 0 
Gene Names: AXIN1AXIN
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens)
Explore O15169 
Go to UniProtKB:  O15169
PHAROS:  O15169
GTEx:  ENSG00000103126 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15169
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
TA [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AC [auth C]
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth A]
AC [auth C],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NB [auth B],
OB [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth A],
N [auth A],
R [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
BA [auth A]
BB [auth B]
CB [auth B]
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
CB [auth B],
DA [auth A],
DB [auth B],
EB [auth B],
F [auth A],
FB [auth B],
G [auth A],
GB [auth B],
H [auth A],
HB [auth B],
I [auth A],
IB [auth B],
J [auth A],
JB [auth B],
KB [auth B],
LB [auth B],
MB [auth B],
O [auth A],
Q [auth A],
S [auth A],
T [auth A],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
WA [auth B],
WB [auth C],
XA [auth B],
XB [auth C],
Y [auth A],
YA [auth B],
YB [auth C],
Z [auth A],
ZA [auth B],
ZB [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
EA [auth A]
FA [auth A]
GA [auth A]
K [auth A]
L [auth A]
EA [auth A],
FA [auth A],
GA [auth A],
K [auth A],
L [auth A],
M [auth A],
P [auth A],
X [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BC [auth C]
CC [auth C]
DC [auth D]
OA [auth A]
PA [auth A]
BC [auth C],
CC [auth C],
DC [auth D],
OA [auth A],
PA [auth A],
PB [auth B],
QA [auth A],
QB [auth B],
RA [auth A],
RB [auth B],
SA [auth A],
SB [auth B],
TB [auth B],
UB [auth B],
VB [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
NA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.585α = 90
b = 195.585β = 90
c = 152.204γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131747
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119156
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM007276

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references
  • Version 1.2: 2024-09-25
    Changes: Database references