8ST9: E3 ligase NleL

Structure of E3 ligase NleL bound to ubiquitin. Determined by X-ray diffraction at 2.5 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Escherichia coli O157:H7 str. Sakai, Homo sapiens
Chains: 4
Atoms: 4,191
Mol. weight: 58.49 kDa
Ligands: AYE
Released: 12 Jul 2023

Explore 8ST9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ST9 contains 34 α-helices and 18 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.

Chain A: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	607-615	9
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	1
β-strand	659-660	2	1
α-helix	662-669	8
α-helix	679-697	19
α-helix	710-726	17
α-helix	728-731	4
α-helix	734-745	12
α-helix	747-749	3
α-helix	754-768	15
α-helix	770-776	7
α-helix	779-781	3

Chain B: 3 helices, 7 β-strands

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

Chain C: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	607-615	9
α-helix	619-627	9
α-helix	628-630	3
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	4
β-strand	659-660	2	4
α-helix	661	1
α-helix	662-669	8
α-helix	679-696	18
α-helix	710-724	15
α-helix	728-731	4
α-helix	734-744	11
α-helix	747-749	3
α-helix	754-768	15
α-helix	770-775	6
α-helix	779-781	3

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SopA	A, C	protein	179	Escherichia coli O157:H7 str. Sakai	A0A0H3JDV8 (AlphaFold model)
Ubiquitin	B, D	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8ST9_1 E3 ubiquitin-protein ligase SopA (chains A, C)
GPNFVSGILDILISDNELKERFIEALNSNKSDYKMIADDQQRKLACVWNPFLDGWELNAQ
HVDMIMGSHVLKDMPLRKQAEILFCLGGVFCKYSSSDMFGTEYDSPEILRRYANGLIEQA
YKTDPQVFGSVYYYNDILDRLQGRNNVFTCTAVLTDMLTEHAKESFPEIFSLYYPVAWR

Sequence of entity 2 (B, D), FASTA

>8ST9_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

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

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 A0A0H3JDV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NB2 2.1 Å, Crystal structure of E. coli O157:H7 effector protein NleL
3NAW 2.5 Å, Crystal structure of E. coli O157:H7 effector protein NleL
3SQV 3.3 Å, Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7

Browse structure collections

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