5CRA: SdeA DUB Domain

Structure of the SdeA DUB Domain. Determined by X-ray diffraction at 2.64 Å resolution. Released 25 Nov 2015.

Method: X-ray diffraction
Resolution: 2.64 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 4
Atoms: 3,859
Mol. weight: 60.09 kDa
Ligands: GVE
Released: 25 Nov 2015

Explore 5CRA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CRA contains 28 α-helices and 42 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 B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	9-10	2	1
β-strand	11	1	2
α-helix	12-21	10
β-strand	30-33	4	3
β-strand	36-38	3	3
α-helix	41-47	7
β-strand	49-56	8	3
β-strand	57	1	4
β-strand	60	1	4
β-strand	62	1	2
β-strand	64-70	7	3
β-strand	75-79	5	3
α-helix	84-88	5
α-helix	91-95	5
α-helix	99	1
β-strand	103-106	4	3
α-helix	109-110	2
α-helix	118-133	16
β-strand	135	1	5
α-helix	138-140	3
α-helix	141-156	16
α-helix	160-171	12

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

Element	Residues	Length	Sheet
β-strand	2-7	6	12
β-strand	12-16	5	12
β-strand	22	1	13
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	12
β-strand	48-49	2	12
α-helix	50-51	2
β-strand	55	1	13
α-helix	57-59	3
β-strand	66-71	6	12
β-strand	74	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SdeA	A, B	protein	193	Legionella pneumophila	Q6RCR0
Polyubiquitin-B	C, D	protein	75	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5CRA_1 SdeA (chains A, B)
MPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHR
DSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLCGY
WVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDP
QLDGKALRENTEK

Sequence of entity 2 (C, D), FASTA

>5CRA_2 Polyubiquitin-B (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
GVE	Methyl 4-aminobutanoate	C5 H11 N O2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination. Sheedlo, M.J., Qiu, J., Tan, Y. et al. Proc Natl Acad Sci U S A (2015) 112:15090-15095. DOI 10.1073/pnas.1514568112 · PubMed

Other PDB entries of the same protein (UniProt Q6RCR0), best resolution first:

5CRB 2.0 Å, Crystal Structure of SdeA DUB
5CRC 2.85 Å, Structure of the SdeA DUB Domain
5YIK 3.1 Å, Structure of a Legionella effector with its substrate
5YIJ 3.18 Å, Structure of a Legionella effector with substrates
5YIM 3.39 Å, Structure of a Legionella effector

Browse structure collections

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