4NM7: GSK-3/Axin complex

Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Mar 2014.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,198
Mol. weight: 47.54 kDa
Ligands: ADP, DTT, MG
Released: 26 Mar 2014

Explore 4NM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NM7 contains 23 α-helices and 15 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	27-30	4	1
β-strand	36-44	9	1
β-strand	52-63	12	1
β-strand	69-75	7	1
β-strand	81-88	8	1
β-strand	93	1	2
α-helix	97-101	5
β-strand	109	1	3
β-strand	112-118	7	1
β-strand	127-133	7	1
β-strand	137-138	2	3
α-helix	139-148	10
α-helix	152-154	3
α-helix	155-173	19
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	296-300	5
α-helix	301-304	4
α-helix	311-318	8
α-helix	325-327	3
α-helix	329-330	2
α-helix	331-335	5
α-helix	338-344	7
α-helix	354-356	3
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	1608	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GSK3B protein	A	protein	377	Homo sapiens	P49841 (AlphaFold model)
Axin-1	B	protein	24	Homo sapiens	O15169 (AlphaFold model)
Phosphorylated Wnt receptor LRP6 e-motif	C	protein	9	Homo sapiens	O75581 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NM7_1 GSK3B protein (chains A)
SCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQ
AKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVL
DYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPD
TAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLL
GQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPE
AIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPP
LATILIPPHARHHHHHH

Sequence of entity 2 (B), FASTA

>4NM7_2 Axin-1 (chains B)
GGILVEPQKFAEELIHRLEAVQRT

Sequence of entity 3 (C), FASTA

>4NM7_3 Phosphorylated Wnt receptor LRP6 e-motif (chains C)
MPPPPSPCT

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1
MG	Magnesium ion	Mg	2

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

Primary citation

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. et al. Elife (2014) 3:e01998-e01998. PubMed

Other PDB entries of the same protein (UniProt P49841 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X2V 1.39 Å, GSK3beta complexed with BiS-3
1O6L 1.6 Å, Crystal structure of an activated Akt/protein kinase B (PKB-PIF chimera) ternary complex…
9X2Q 1.68 Å, GSK3beta complexed with BiS-1
1O6K 1.7 Å, Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
9X2X 1.79 Å, GSK3beta complexed with BiS-5
1J1B 1.8 Å, Binary complex structure of human tau protein kinase I with AMPPNP
2JDO 1.8 Å, Structure of pkb-beta (AKT2) complexed with isoquinoline-5-sulfonic acid…
7SXJ 1.85 Å, BIO-2895 (BRD0705) bound GSK3beta-axin complex
3QKL 1.9 Å, Spirochromane Akt Inhibitors
9X2W 1.92 Å, GSK3beta complexed with BiS-4
2X39 1.93 Å, Structure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin-…
1Q5K 1.94 Å, crystal structure of Glycogen synthase kinase 3 in complexed with inhibitor

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