8RU4: Human Catenin Beta-1

Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor. Determined by X-ray diffraction at 2.13 Å resolution. Released 4 Sept 2024.

Method: X-ray diffraction
Resolution: 2.13 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,174
Mol. weight: 117.3 kDa
Ligands: GLC
Released: 4 Sept 2024

Explore 8RU4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RU4 contains 78 α-helices and 4 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: 39 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	153-160	8
α-helix	165-178	14
α-helix	182-190	9
α-helix	194-204	11
α-helix	208-221	14
α-helix	225-233	9
α-helix	236-242	7
α-helix	243-245	3
α-helix	249-265	17
α-helix	269-275	7
α-helix	278-284	7
α-helix	285-287	3
α-helix	291-305	15
α-helix	309-317	9
α-helix	320-330	11
α-helix	334-347	14
α-helix	353-359	7
α-helix	362-367	6
α-helix	375-388	14
α-helix	389-391	3
α-helix	399-408	10
α-helix	414-428	15
α-helix	432-440	9
α-helix	443-454	12
α-helix	458-471	14
α-helix	478-487	10
α-helix	491-496	6
α-helix	504-517	14
α-helix	521-523	3
α-helix	524-529	6
α-helix	532-549	18
β-strand	561	1	1
β-strand	564	1	1
α-helix	566-580	15
α-helix	584-592	9
α-helix	596-601	6
α-helix	602-604	3
α-helix	608-621	14
α-helix	625-633	9
α-helix	637-643	7
α-helix	649-662	14

Chain B: 38 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	154-158	5
α-helix	168-180	13
α-helix	186-190	5
α-helix	195-203	9
α-helix	208-221	14
α-helix	225-233	9
α-helix	236-242	7
α-helix	243-245	3
α-helix	249-265	17
α-helix	269-275	7
α-helix	278-284	7
α-helix	285-287	3
α-helix	291-305	15
α-helix	309-317	9
α-helix	320-330	11
α-helix	334-347	14
α-helix	353-359	7
α-helix	362-367	6
α-helix	375-388	14
α-helix	389-391	3
α-helix	399-408	10
α-helix	414-428	15
α-helix	432-440	9
α-helix	443-454	12
α-helix	458-471	14
α-helix	478-487	10
α-helix	491-496	6
α-helix	504-517	14
α-helix	521-523	3
α-helix	524-529	6
α-helix	532-549	18
β-strand	561	1	2
β-strand	564	1	2
α-helix	566-580	15
α-helix	584-592	9
α-helix	596-601	6
α-helix	608-621	14
α-helix	625-633	9
α-helix	637-643	7
α-helix	649-663	15

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Catenin beta-1	A, B	protein	523	Homo sapiens	P35222 (AlphaFold model)
Axin-1	C	protein	13	Homo sapiens	O15169 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8RU4_1 Catenin beta-1 (chains A, B)
GPDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEASRHAIMRSPQMVSAIVRTM
QNTNDVETARCTAGTLHNLSHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNL
LLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQ
ALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCL
WTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVG
GIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPS
HWPLIKATVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGGTQQQFVE
GVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELA
QDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRMSED

Sequence of entity 2 (C), FASTA

>8RU4_2 Axin-1 (chains C)
XXILDXHLXRVWX

Ligands and cofactors

ID	Name	Formula	Copies
GLC	alpha-D-glucopyranose	C6 H12 O6	7

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

Primary citation

Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene beta-Catenin. Yeste-Vazquez, A., Paulussen, F.M., Wendt, M. et al. Angew Chem Int Ed Engl (2024) 63:e202411749-e202411749. DOI 10.1002/anie.202411749 · PubMed

Other PDB entries of the same protein (UniProt P35222 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FQN 1.65 Å, Phosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted…
3FQR 1.7 Å, Phosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted…
7AFW 1.81 Å, Beta-Catenin in complex with compound 6
1JDH 1.9 Å, Crystal structure of beta-catenin and htcf-4
9I8K 2.0 Å, Beta-catenin armadillo (150-663)
9I8X 2.0 Å, Beta-catenin armadillo with cyclic peptide and Compound 2
8RU3 2.0 Å, Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor
6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
29KL 2.09 Å, Crystal structure of Human Catenin Beta-1 in complex with cyclic beta sheet peptide…
1G3J 2.1 Å, Crystal structure of the XTCF3-cbd/beta-catenin armadillo repeat complex
1T08 2.1 Å, Crystal structure of beta-catenin/ICAT helical domain/unphosphorylated APC R3
3DIW 2.1 Å, c-terminal beta-catenin bound TIP-1 structure

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