6W9R: OTU deubiquitinase from Wolbachia pipientis wMel

Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin. Determined by X-ray diffraction at 1.82 Å resolution. Released 1 Jul 2020.

Method: X-ray diffraction
Resolution: 1.82 Å
Organisms: Homo sapiens, Wolbachia pipientis wMel
Chains: 24
Atoms: 26,594
Mol. weight: 335.41 kDa
Ligands: FLC
Released: 1 Jul 2020

Explore 6W9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9R contains 126 α-helices and 192 β-strands across 24 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, D, E and F: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	25
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	26
β-strand	106	1	26
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	27
β-strand	152-161	10	27
β-strand	164-168	5	27
β-strand	181-186	6	27
β-strand	192-194	3	27
β-strand	195-197	3	25

Chains B and C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	39-41	3
β-strand	42-44	3	28
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	29
β-strand	106	1	29
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	30
β-strand	152-161	10	30
β-strand	164-168	5	30
β-strand	181-186	6	30
β-strand	192-194	3	30
β-strand	195-197	3	28

Chain G: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	43
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	44
β-strand	105-107	3	44
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	45
β-strand	152-161	10	45
β-strand	164-168	5	45
β-strand	181-186	6	45
β-strand	192-194	3	45
β-strand	195-197	3	43

Chain H: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	46
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	47
β-strand	105-107	3	47
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	48
β-strand	152-161	10	48
β-strand	164-167	4	48
β-strand	181-186	6	48
β-strand	192-194	3	48
β-strand	195-197	3	46

Chain I: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	49
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-96	8
β-strand	98	1	50
β-strand	106	1	50
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	51
β-strand	152-161	10	51
β-strand	164-168	5	51
β-strand	181-186	6	51
β-strand	192-194	3	51
β-strand	195-197	3	49

Chain J: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	39-41	3
β-strand	42-44	3	52
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	53
β-strand	106	1	53
α-helix	110-116	7
α-helix	123-125	3
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	54
β-strand	152-161	10	54
β-strand	164-168	5	54
β-strand	181-186	6	54
β-strand	192-194	3	54
β-strand	195-197	3	52

Chain K: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	42-44	3	55
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	44
β-strand	105-107	3	44
α-helix	110-116	7
α-helix	123-125	3
α-helix	129-137	9
β-strand	140-149	10	56
β-strand	152-161	10	56
β-strand	164-167	4	56
β-strand	181-186	6	56
β-strand	192-194	3	56
β-strand	195-197	3	55

Chain L: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	39-41	3
β-strand	42-44	3	57
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-95	7
β-strand	98	1	47
β-strand	105-107	3	47
α-helix	110-116	7
α-helix	126-130	5
α-helix	131-137	7
β-strand	140-149	10	58
β-strand	152-161	10	58
β-strand	164-168	5	58
β-strand	181-186	6	58
β-strand	192-194	3	58
β-strand	195-197	3	57

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	M, N, O, P, Q, R, S, T, U, V, W, X	protein	78	Homo sapiens	F5H388 (AlphaFold model)
OTU domain-containing protein wMelOTU	A, B, C, D, E, F, G, H, I, J, K, L	protein	168	Wolbachia pipientis wMel	A0A8X6FBF0 (AlphaFold model)

Sequence of entity 1 (M, N, O, P, Q, R, S, T, U, V, W, X), FASTA

>6W9R_1 Ubiquitin (chains M, N, O, P, Q, R, S, T, U, V, W, X)
GPMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGX

Sequence of entity 2 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>6W9R_2 OTU domain-containing protein wMelOTU (chains A, B, C, D, E, F, G, H, I, J, K, L)
GPDNFYVGQAIGNGSCFFDSFRQSLEQQTGEQVTAEKLRNDCREFAQKNPPKWFTNAIVN
SHDNNGQHRSETVDNYTADIMRNSRWGDPDVEGRILCEKYKVKLHVIENQTVDNQDLSLH
ELIDNSGSKSAGEYNKVDYDDSSTVHIINKGGLHFEPLLDRNKSSAKQ

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	12

Primary citation

Identification and characterization of diverse OTU deubiquitinases in bacteria. Schubert, A.F., Nguyen, J.V., Franklin, T.G. et al. EMBO J (2020) 39:e105127-e105127. DOI 10.15252/embj.2020105127 · PubMed

Other PDB entries of the same protein (UniProt F5H388 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ST7 1.44 Å, Structure of E3 ligase VsHECT bound to ubiquitin
4I6N 1.7 Å, Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin…
8RQI 1.94 Å, Structure of Rhizobium NopD with ubiquitin
4IG7 2.0 Å, Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester
4PQT 2.05 Å, Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal…
6W9S 2.1 Å, Crystal structure of an OTU deubiquitinase from Escherichia albertii bound to ubiquitin
9FN4 2.15 Å, DUBS Parachlamydia sp. PcJOS
9FPA 2.18 Å, DUBS Parachlamydia sp. PcJOS orthorhombic crystal form
6NN6 3.9 Å, Structure of Dot1L-H2BK120ub nucleosome complex

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