8VMF: Transition-state mimic of the GSK-3/Axin complex

Crystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,226
Mol. weight: 48.04 kDa
Ligands: MG, AF3, ADP
Released: 28 Aug 2024

Explore 8VMF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VMF contains 23 α-helices and 17 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	1
β-strand	36-44	9	1
β-strand	52-65	14	1
β-strand	68-75	8	1
β-strand	81-87	7	1
β-strand	93	1	2
α-helix	97-102	6
β-strand	109	1	3
β-strand	112-119	8	1
β-strand	126-133	8	1
β-strand	137-138	2	3
α-helix	139-148	10
α-helix	155-174	20
β-strand	177-178	2	4
α-helix	184-186	3
β-strand	187-190	4	3
β-strand	195-198	4	3
β-strand	205-206	2	4
α-helix	225-228	4
α-helix	237-252	16
α-helix	262-273	12
α-helix	276-277	2
α-helix	278-284	7
α-helix	286-288	3
α-helix	297-300	4
α-helix	301-304	4
α-helix	311-320	10
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-340	3
β-strand	349	1	5
α-helix	354	1
β-strand	355	1	5
α-helix	356	1
α-helix	371-373	3
α-helix	374-377	4
α-helix	380-382	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	385-399	15

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	46	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycogen synthase kinase-3 beta	A	protein	364	Mus musculus	Q9WV60 (AlphaFold model)
Axin-1	B	protein	24	Homo sapiens	O15169 (AlphaFold model)
Catenin beta-1	C	protein	28	Homo sapiens	P35222 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VMF_1 Glycogen synthase kinase-3 beta (chains A)
MKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIK
KVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARH
YSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAK
QLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQ
LVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTP
TARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARHH
HHHH

Sequence of entity 2 (B), FASTA

>8VMF_2 Axin-1 (chains B)
GGILVEPQKFAEELIHRLEAVQRT

Sequence of entity 3 (C), FASTA

>8VMF_3 Catenin beta-1 (chains C)
MIHSGATTTAPDLSGKGNPEEEDVDTSQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AF3	Aluminum fluoride	Al F3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3 beta. Enos, M.D., Gavagan, M., Jameson, N. et al. Sci Signal (2024) 17. DOI 10.1126/scisignal.ado0881 · PubMed

Other PDB entries of the same protein (UniProt Q9WV60 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AE3 2.14 Å, Crystal structure of GSK3beta complexed with Morin
8VME 2.3 Å, Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A…
8VMG 2.45 Å, Crystal structure of GSK-3 26-383 bound to Axin 383-435
4NU1 2.5 Å, Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to…
5AIR 2.53 Å, Structural analysis of mouse GSK3beta fused with LRP6 peptide.

Browse structure collections

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