7M3Q: E3 ubiquitin-protein ligase SMURF2

Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV). Determined by X-ray diffraction at 2.5 Å resolution. Released 21 Apr 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,738
Mol. weight: 57.44 kDa
Ligands: DTT
Released: 21 Apr 2021

Explore 7M3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M3Q contains 24 α-helices and 22 β-strands across 2 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	370-386	17
β-strand	392-397	6	1
α-helix	402-412	11
α-helix	415-418	4
β-strand	421-426	6	1
α-helix	434-450	17
α-helix	452-454	3
β-strand	457-459	3	2
β-strand	467-469	3	2
α-helix	471-475	5
α-helix	479-495	17
β-strand	504	1	2
α-helix	506-512	7
α-helix	515-517	3
α-helix	522-525	4
α-helix	527-538	12
β-strand	548	1	3
β-strand	550-554	5	4
β-strand	559-563	5	4
α-helix	568-570	3
β-strand	572	1	3
α-helix	578-591	14
α-helix	595-608	14
α-helix	611-614	4
α-helix	619-627	9
β-strand	629	1	5
α-helix	634-639	6
β-strand	641-644	4	6
α-helix	651-662	12
α-helix	665-676	12
β-strand	681	1	5
α-helix	686-688	3
β-strand	690	1	7
β-strand	695	1	7
β-strand	698-702	5	6
α-helix	710-711	2
β-strand	712-714	3	6
β-strand	719-722	4	6
α-helix	728-738	11

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-16	5	8
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-44	4	8
β-strand	49	1	8
β-strand	66-71	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SMURF2	A	protein	387	Homo sapiens	Q9HAU4 (AlphaFold model)
Ubiquitin variant	B	protein	98	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M3Q_1 E3 ubiquitin-protein ligase SMURF2 (chains A)
GAMAPRYKRDLVQKLKILRQELSQQQPQAGHCRIEVSREEIFEESYRQVMKMRPKDLWKR
LMIKFRGEEGLDYGGVAREWLYLLSHEMLNPYYGLFQYSRDDIYTLQINPDSAVNPEHLS
YFHFVGRIMGMAVFHGHYIDGGFTLPFYKQLLGKSITLDDMELVDPDLHNSLVWILENDI
TGVLDHTFCVEHNAYGEIIQHELKPNGKSIPVNEENKKEYVRLYVNWRFLRGIEAQFLAL
QKGFNEVIPQHLLKTFDEKELELIICGLGKIDVNDWKVNTRLKHCTPDSNIVKWFWKAVE
FFDEERRARLLQFVTGSSRVPLQGFKALQGAAGPRLFTIHQIDACTNNLPKAHTCFNRID
IPPYESYEKLYEKLLTAIEETCGFAVE

Sequence of entity 2 (B), FASTA

>7M3Q_2 Ubiquitin variant (chains B)
MAHHHHHHVTSLYKKAGDYKDDDKMLIFVWTFKGNTITLEVEPSDTIENVKAKIQDKEGI
PPDQQRLIFARKQLEDGRTLSDYNILKESTLLLVRRLR

Ligands and cofactors

ID	Name	Formula	Copies
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1

Water and common crystallization additives (EDO, CL, NA, SO4) are not listed.

Primary citation

Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV). Chowdhury, A., Singer, A.U., Ogunjimi, A.A. et al. To be published.

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
6FX4 2.5 Å, Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C
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

Browse structure collections

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