5WZZ: E3 ubiquitin-protein ligase SIAH1

Name: PDB 5WZZ: The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation
Published: 2017-08-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation. Determined by X-ray diffraction at 2.1 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,512
Mol. weight: 96.05 kDa
Ligands: ZN
Released: 16 Aug 2017

Explore 5WZZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WZZ contains 43 α-helices and 67 β-strands across 8 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: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	96-97	2	1
α-helix	101-103	3
β-strand	108-109	2	1
α-helix	111-120	10
α-helix	125	1
β-strand	126-127	2	2
α-helix	128	1
β-strand	138-139	2	2
α-helix	141-143	3
α-helix	144-151	8
β-strand	157-159	3	3
β-strand	162-167	6	4
β-strand	176-184	9	3
β-strand	187-197	11	3
β-strand	203-211	9	3
α-helix	215-218	4
β-strand	221-229	9	4
β-strand	232-238	7	4
α-helix	239-240	2
β-strand	241-242	2	3
α-helix	248-252	5
β-strand	257-260	4	3
α-helix	261-267	7
β-strand	268-269	2	4
β-strand	272-281	10	4

Chain B: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	95-97	3	5
α-helix	99-103	5
β-strand	108-110	3	5
α-helix	111-113	3
α-helix	114-120	7
α-helix	125	1
β-strand	126-127	2	6
α-helix	128	1
β-strand	138-139	2	6
α-helix	141-143	3
α-helix	144-151	8
β-strand	157-159	3	7
β-strand	162-167	6	8
β-strand	177-184	8	7
β-strand	187-197	11	7
β-strand	203-211	9	7
α-helix	215-218	4
β-strand	221-229	9	8
β-strand	232-238	7	8
α-helix	239-240	2
β-strand	241-242	2	7
α-helix	248-252	5
β-strand	257-260	4	7
α-helix	261-267	7
β-strand	269	1	9
β-strand	272	1	9
β-strand	273-281	9	8

Chain C: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	96-97	2	10
α-helix	99-103	5
β-strand	108-109	2	10
α-helix	111-120	10
α-helix	125	1
β-strand	126-127	2	11
α-helix	128	1
β-strand	138-139	2	11
α-helix	141-143	3
α-helix	144-151	8
β-strand	157-159	3	12
β-strand	162-167	6	13
β-strand	176-184	9	12
β-strand	187-198	12	12
β-strand	202-211	10	12
α-helix	215-218	4
β-strand	221-229	9	13
β-strand	232-238	7	13
α-helix	239-240	2
β-strand	241-242	2	12
α-helix	248-252	5
β-strand	257-260	4	12
α-helix	261-267	7
β-strand	269	1	14
β-strand	272	1	14
β-strand	273-281	9	13

Chain D: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	95-97	3	15
α-helix	99-103	5
β-strand	108-110	3	15
α-helix	111-120	10
α-helix	125	1
β-strand	126-127	2	16
α-helix	128	1
β-strand	138-139	2	16
α-helix	141-143	3
α-helix	144-151	8
β-strand	157-159	3	17
β-strand	162-167	6	8
β-strand	176-184	9	17
β-strand	187-199	13	17
β-strand	202-211	10	17
α-helix	215-218	4
β-strand	221-228	8	8
β-strand	233-238	6	8
α-helix	239-240	2
β-strand	241-242	2	17
α-helix	248-252	5
β-strand	257-260	4	17
α-helix	261-267	7
β-strand	269	1	18
β-strand	272	1	18
β-strand	273-281	9	8

Chains E and H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	379-383	5	13
α-helix	384-386	3

Chains F and G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	380-383	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SIAH1	A, B, C, D	protein	190	Homo sapiens	Q8IUQ4 (AlphaFold model)
Axin-1	E, F, G, H	protein	20	Homo sapiens	O15169 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5WZZ_1 E3 ubiquitin-protein ligase SIAH1 (chains A, B, C, D)
SVLFPCKYASSGCEITLPHTEKADHEELCEFRPYSCPCPGASCKWQGSLDAVMPHLMHQH
KSITTLQGEDIVFLATDINLPGAVDWVMMQSCFGFHFMLVLEKQEKYDGHQQFFAIVQLI
GTRKQAENFAYRLELNGHRRRLTWEATPRSIHEGIATAIMNSDCLVFDTSIAQLFAENGN
LGINVTISMC

Sequence of entity 2 (E, F, G, H), FASTA

>5WZZ_2 Axin-1 (chains E, F, G, H)
YRVPKEVRVEPQKFAEELIH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation. Ji, L., Jiang, B., Jiang, X. et al. Genes Dev (2017) 31:904-915. DOI 10.1101/gad.300053.117 · PubMed

Other PDB entries of the same protein (UniProt Q8IUQ4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CA1 1.58 Å, Crystal structure of Siah1 at 1.58 A resolution.
9G0L 1.9 Å, Crystal structure of the RING-ZnF1 fragment of SIAH1
4C9Z 1.95 Å, Crystal structure of Siah1 at 1.95 A resolution
2A25 2.2 Å, Crystal structure of Siah1 SBD bound to the peptide EKPAAVVAPITTG from SIP
4X3G 2.34 Å, Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide
4I7D 2.4 Å, Siah1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR
8HEO 2.53 Å, Crystal structure of SIAH1 SBD bound to Axin2 peptide
4I7C 2.8 Å, Siah1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR
4I7B 3.0 Å, Siah1 bound to synthetic peptide (ACE)KLRPV(ABA)MVRPTVR

Browse structure collections

About this viewer

MolViewer shows 5WZZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.