8VME

Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide

PDB DOI: https://doi.org/10.2210/pdb8VME/pdb

Classification: TRANSFERASE/SIGNALING PROTEIN
Organism(s): Mus musculus, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-01-13 Released: 2024-08-28
Deposition Author(s): Enos, M.D., Gavagan, M., Jameson, N., Zalatan, J.G., Weis, W.I.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.230
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional effects of phosphopriming and scaffolding in the kinase GSK3beta

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

(2024) Sci Signal

DOI: https://doi.org/10.1126/scisignal.ado0881

Macromolecule Content

Total Structure Weight: 48.37 kDa
Atom Count: 3,308
Modelled Residue Count: 383
Deposited Residue Count: 417
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A	365	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WV60
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin-1	B	24	Homo sapiens	Mutation(s): 0 Gene Names: Axin1, Axin, Fu
UniProt
Find proteins for O35625 (Mus musculus) Explore O35625 Go to UniProtKB: O35625
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35625
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Catenin beta-1	C	28	Homo sapiens	Mutation(s): 1 Gene Names: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens) Explore P35222 Go to UniProtKB: P35222
PHAROS: P35222 GTEx: ENSG00000168036
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35222
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.230
R-Value Observed: 0.183
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.257	α = 90
b = 82.257	β = 90
c = 280.99	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
pointless	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131747
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119156
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM007276