8ST8: E3 ligase SopA

Structure of E3 ligase SopA bound to ubiquitin. Determined by X-ray diffraction at 1.75 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Salmonella enterica subsp. enterica serovar Typhimurium, Homo sapiens
Chains: 2
Atoms: 2,383
Mol. weight: 30.59 kDa
Ligands: AYE
Released: 12 Jul 2023

Explore 8ST8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ST8 contains 18 α-helices and 7 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	593-595	3
α-helix	597-612	16
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
α-helix	656-658	3
α-helix	662-671	10
α-helix	679-697	19
α-helix	710-726	17
α-helix	728-730	3
α-helix	734-745	12
α-helix	754-768	15
α-helix	770-776	7
α-helix	779-781	3

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	56-59	4
β-strand	66-70	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SopA	A	protein	197	Salmonella enterica subsp. enterica serovar Typhimurium	Q8ZNR3 (AlphaFold model)
Ubiquitin	B	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8ST8_1 E3 ubiquitin-protein ligase SopA (chains A)
HHHHHHSSGLEVLFQGPRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDDASVS
RLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAIFGTE
HDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSMQRHA
RKYFPSVLSSILPLAWA

Sequence of entity 2 (B), FASTA

>8ST8_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
AYE	prop-2-en-1-amine	C3 H7 N	1

Primary citation

Bacterial ligases reveal fundamental principles of polyubiquitin specificity. Franklin, T.G., Brzovic, P.S., Pruneda, J.N. Mol Cell (2023) 83:4538-4554.e4. DOI 10.1016/j.molcel.2023.11.017 · PubMed

Other PDB entries of the same protein (UniProt Q8ZNR3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QYU 2.1 Å, Crystal structure of Salmonella effector protein SopA
2QZA 2.8 Å, Crystal structure of Salmonella effector protein SopA
5JW7 2.85 Å, Crystal structure of SopA-Trim56 complex
3SY2 3.27 Å, Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human…

Browse structure collections

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