6FX4: E3 ubiquitin-protein ligase SMURF2

Name: PDB 6FX4: Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C
Published: 2018-07-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,203
Mol. weight: 45.32 kDa
Released: 11 Jul 2018

Explore 6FX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FX4 contains 22 α-helices and 28 β-strands across 4 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.

Chains A and C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
β-strand	11-14	4	1
α-helix	21-32	12
α-helix	35-46	12
α-helix	50-52	3
α-helix	56-58	3
β-strand	60-61	2	2
β-strand	64-65	2	2
β-strand	68-72	5	1
α-helix	80-81	2
β-strand	82-84	3	1
β-strand	89-92	4	1
α-helix	98-110	13

Chains B and D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3
β-strand	74	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SMURF2	A, C	protein	122	Homo sapiens	Q9HAU4 (AlphaFold model)
Polyubiquitin-B	B, D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6FX4_1 E3 ubiquitin-protein ligase SMURF2 (chains A, C)
GAMGKIDVNDWKVNTRLKHATPDSNIVKWFWKAVEFFDEERRARLLQFVTGSSRVPLQGF
KALQGAAGPRLFTIHQIDANTNNLPKAHTCFNRIDIPPYESYEKLYEKLLTAIEETSGFA
VE

Sequence of entity 2 (B, D), FASTA

>6FX4_2 Polyubiquitin-B (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Primary citation

beta-Sheet Augmentation Is a Conserved Mechanism of Priming HECT E3 Ligases for Ubiquitin Ligation. Jackl, M., Stollmaier, C., Strohaker, T. et al. J Mol Biol (2018) 430:3218-3233. DOI 10.1016/j.jmb.2018.06.044 · PubMed

Other PDB entries of the same protein (UniProt Q9HAU4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FSH 2.08 Å, Crystal structure of the HECT domain of Smurf 2 in complex with inhibitor 8
1ZVD 2.1 Å, Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT domain
7M3Q 2.5 Å, Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)
2DJY Solution structure of Smurf2 WW3 domain-Smad7 PY peptide complex
2JQZ Solution Structure of the C2 domain of human Smurf2
2KXQ Solution Structure of Smurf2 WW2 and WW3 bound to Smad7 PY motif containing peptide
2LTZ Smurf2 WW3 domain in complex with a Smad7 derived peptide

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