6UPU: Orientia tsutsugamushi OtDUB

Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin. Determined by X-ray diffraction at 2.2 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Orientia tsutsugamushi (strain Ikeda), Homo sapiens
Chains: 16
Atoms: 15,824
Mol. weight: 221.86 kDa
Released: 1 Apr 2020

Explore 6UPU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UPU contains 107 α-helices and 128 β-strands across 16 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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	12-13	2
β-strand	14-15	2	1
α-helix	16-27	12
β-strand	33-35	3	2
β-strand	40	1	2
α-helix	44-60	17
β-strand	65-71	7	2
β-strand	77-84	8	2
β-strand	90-95	6	2
β-strand	98	1	3
α-helix	102-104	3
α-helix	106-115	10
β-strand	120-123	4	2
β-strand	127	1	3
α-helix	135-147	13
α-helix	150-154	5
α-helix	155-191	37
β-strand	197-198	2	4
α-helix	199-208	10
α-helix	214-225	12
β-strand	234-235	2	4
α-helix	237-245	9
α-helix	248-257	10

Chains B and J: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
β-strand	12-17	6	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-69	4	5
α-helix	71-73	3
β-strand	74-75	2	1

Chains C, G, L and O: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7
α-helix	72-73	2

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-71	6	9
α-helix	72	1

Chains E and M: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	15	1	11
α-helix	16-27	12
β-strand	33-35	3	12
β-strand	40	1	12
α-helix	44-59	16
β-strand	65-71	7	12
β-strand	77-84	8	12
β-strand	90-95	6	12
α-helix	102-104	3
α-helix	106-115	10
β-strand	120-123	4	12
α-helix	135-147	13
α-helix	150-154	5
α-helix	155-191	37
β-strand	196-198	3	13
α-helix	199-208	10
α-helix	214-225	12
β-strand	234-236	3	13
α-helix	237-245	9
α-helix	248-258	11

Chains F and N: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	14
β-strand	12-17	6	14
β-strand	22	1	15
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	14
β-strand	48-49	2	14
β-strand	55	1	15
α-helix	57-59	3
β-strand	66-69	4	14
α-helix	71-73	3
β-strand	74	1	11

Chains H, K and P: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	18
β-strand	12-17	6	18
β-strand	22	1	19
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	18
β-strand	48-49	2	18
α-helix	50-51	2
β-strand	55	1	19
α-helix	57-59	3
β-strand	66-71	6	18
α-helix	72-73	2

Chain I: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	12-13	2
β-strand	14-15	2	20
α-helix	16-27	12
β-strand	33-35	3	21
β-strand	40	1	21
α-helix	44-60	17
β-strand	65-71	7	21
β-strand	77-84	8	21
β-strand	90-95	6	21
β-strand	98	1	22
α-helix	106-115	10
β-strand	120-123	4	21
β-strand	127	1	22
α-helix	135-147	13
α-helix	150-154	5
α-helix	155-191	37
β-strand	197-198	2	23
α-helix	199-208	10
α-helix	214-225	12
β-strand	234-235	2	23
α-helix	237-245	9
α-helix	248-258	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ULP_PROTEASE domain-containing protein	A, E, I, M	protein	260	Orientia tsutsugamushi (strain Ikeda)	B3CVM3
Ubiquitin	B, C, D, F, G, H, J, K, L, N, O, P	protein	79	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, E, I, M), FASTA

>6UPU_1 ULP_PROTEASE domain-containing protein (chains A, E, I, M)
GMANDQDLSNPEYLYTEDDINQLLKHYLGLDDRISIIQHVALNESLLLKQTLHQVLSDIF
SGMQEKAVIPLHTGNNHWVAMAIKKGMNDDIVISYNDPMGVSIDDKVTLINCIKELCPGA
KINDLQTVQQTNVYDCGPFVVDNLIKMSQGQPILSTEEAKQQAQNIRQSQVNFLSENRMI
TSAAAALADTLLKNNNRITEGVLVDRIFDNKILSVQEKQQLLNNLLDNHIKENKSLTKES
LTRMLASTHFVQQQANVLLN

Sequence of entity 2 (B, C, D, F, G, H, J, K, L, N, O, P), FASTA

>6UPU_2 Ubiquitin (chains B, C, D, F, G, H, J, K, L, N, O, P)
GGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Primary citation

A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi. Berk, J.M., Lim, C., Ronau, J.A. et al. Nat Commun (2020) 11:2343-2343. DOI 10.1038/s41467-020-15985-4 · PubMed

Other PDB entries of the same protein (UniProt B3CVM3), best resolution first:

6X1G 1.6 Å, Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in…
6UPS 2.0 Å, Crystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein…
6X1H 2.91 Å, Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia…

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