8EFW: SdeA

Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin. Determined by X-ray diffraction at 2.81 Å resolution. Released 20 Sept 2023.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 2
Atoms: 1,851
Mol. weight: 30.33 kDa
Released: 20 Sept 2023

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

Secondary structure: helices and β-sheets

8EFW contains 16 α-helices and 16 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 B: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	10-11	2	1
α-helix	12-22	11
α-helix	27-29	3
β-strand	30-33	4	2
β-strand	36-38	3	2
α-helix	41-47	7
β-strand	49-56	8	2
β-strand	62-63	2	1
β-strand	64-70	7	2
β-strand	75-79	5	2
α-helix	84-95	12
α-helix	99	1
β-strand	103-106	4	2
α-helix	109-110	2
α-helix	120-121	2
α-helix	122-126	5
α-helix	127-133	7
α-helix	138-140	3
α-helix	141-154	14
α-helix	158-169	12

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	3
β-strand	49	1	3
α-helix	50-51	2
β-strand	55	1	4
β-strand	66-71	6	3
β-strand	74-75	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SdeA	B	protein	200	Legionella pneumophila	Q5ZTK4 (AlphaFold model)
Ubiquitin	C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8EFW_1 SdeA (chains B)
PLGSMPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGV
GPHRDSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMG
LCGYWVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFP
EGEPQLDGKALRENTEKDLK

Sequence of entity 2 (C), FASTA

>8EFW_2 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Primary citation

Cocrystallization of ubiquitin-deubiquitinase complexes through disulfide linkage. Negron Teron, K.I., Das, C. Acta Crystallogr D Struct Biol (2023) 79:1044-1055. DOI 10.1107/S2059798323008501 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YSI 1.55 Å, SdeA mART-C domain EE/AA NCA complex
9R3T 1.98 Å, C-terminal domain of SdeA Legionella effector
5YSJ 2.06 Å, SdeA mART-C domain WT apo
6B7Q 2.2 Å, Crystal structure of Legionella effector protein sdeA (lpg2157) aa. 211-910
5YSK 2.4 Å, SdeA mART-C domain EE/AA apo
7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6WTG 2.63 Å, SdeA DUB Domain in complex with Ubiquitin
6G0C 2.8 Å, Crystal structure of SdeA catalytic core
7PPO 2.91 Å, Structure of SidJ/CaM bound to SdeA in pre-glutamylation state
7PQE 3.7 Å, Structure of SidJ/CaM bound to SdeA in post-catalysis state

Browse structure collections

About this viewer

MolViewer shows 8EFW 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.