3VON: Crystalstructure of the ubiquitin protease

Crystalstructure of the ubiquitin protease. Determined by X-ray diffraction at 3.15 Å resolution. Released 30 May 2012.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 42
Atoms: 51,450
Mol. weight: 742.23 kDa
Released: 30 May 2012

Explore 3VON in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VON contains 362 α-helices and 350 β-strands across 42 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-35	5	3
β-strand	45-51	7	3
α-helix	52-53	2
β-strand	62-68	7	3
α-helix	77-78	2
β-strand	79-82	4	3
β-strand	84	1	4
β-strand	91	1	5
β-strand	97	1	3
β-strand	98	1	5
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-125	11
α-helix	135-138	4
β-strand	142	1	4

Chain A: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	1
β-strand	52-53	2	2
α-helix	54-59	6
α-helix	70-76	7
β-strand	81-83	3	2
β-strand	85	1	1
α-helix	91-103	13
α-helix	108-126	19
α-helix	132-150	19
α-helix	155-162	8
α-helix	165-185	21
α-helix	187-190	4
α-helix	191-193	3
α-helix	200-203	4
α-helix	204-208	5
α-helix	217-227	11
β-strand	231-235	5	2
β-strand	247-249	3	2
α-helix	254-255	2
β-strand	257-262	6	2
β-strand	265-269	5	2

Chain b: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	9
β-strand	31-40	10	9
α-helix	41-42	2
β-strand	51-57	7	9
α-helix	66-67	2
β-strand	68-71	4	9
β-strand	77	1	10
β-strand	80	1	10
β-strand	85	1	9
β-strand	86	1	10
α-helix	89-91	3
α-helix	101-113	13
α-helix	126-131	6
α-helix	133-147	15

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-24	14
β-strand	31-32	2	6
β-strand	35	1	6
β-strand	45-51	7	6
α-helix	52-53	2
β-strand	62-68	7	6
α-helix	77-78	2
β-strand	79-82	4	6
β-strand	84	1	7
β-strand	91	1	8
β-strand	97	1	6
β-strand	98	1	8
α-helix	104-107	4
α-helix	115-125	11
α-helix	137-138	2
β-strand	142	1	7

Chain c: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	48	1	13
β-strand	52-53	2	14
α-helix	54-59	6
α-helix	69-76	8
β-strand	81-83	3	14
β-strand	85	1	13
α-helix	91-103	13
α-helix	108-127	20
α-helix	132-150	19
α-helix	155-159	5
α-helix	165-185	21
α-helix	187-190	4
α-helix	191-193	3
α-helix	200-203	4
α-helix	204-208	5
α-helix	217-227	11
β-strand	231-235	5	14
β-strand	245-249	5	14
α-helix	254-255	2
β-strand	257-262	6	14
β-strand	265-269	5	14

Chain C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	11
α-helix	28	1
β-strand	34-40	7	11
α-helix	41-42	2
β-strand	51-57	7	11
α-helix	66-67	2
β-strand	68-71	4	11
β-strand	80	1	12
β-strand	85	1	11
β-strand	86	1	12
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-130	7
α-helix	133-143	11
α-helix	144-148	5

Chain d: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-32	2	18
β-strand	35	1	18
β-strand	45-51	7	18
α-helix	52-53	2
β-strand	62-68	7	18
α-helix	77-78	2
β-strand	79-82	4	18
β-strand	84	1	19
β-strand	91	1	20
β-strand	97	1	18
β-strand	98	1	20
α-helix	99	1
α-helix	115-125	11
α-helix	129-132	4
α-helix	137-138	2
β-strand	142	1	19

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-24	14
β-strand	31-35	5	15
β-strand	45-51	7	15
α-helix	52-53	2
β-strand	62-68	7	15
β-strand	79-82	4	15
β-strand	84	1	16
β-strand	91	1	17
β-strand	97	1	15
β-strand	98	1	17
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-125	11
α-helix	137-138	2
β-strand	142	1	16

32 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 thioesterase OTUB1	A, H, O, V, c, j	protein	228	Homo sapiens	Q96FW1 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 variant 2	B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o	protein	138	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p	protein	148	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (A, H, O, V, c, j), FASTA

>3VON_1 Ubiquitin thioesterase OTUB1 (chains A, H, O, V, c, j)
SNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEA
LLDDSKELQRFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEKQTSVADLLASFN
DQSTSDYLVVYLRLLTSGYLQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIAL
AQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPKVYLLYRPGHYDILYK

Sequence of entity 2 (B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o), FASTA

>3VON_2 Ubiquitin-conjugating enzyme E2 variant 2 (chains B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o)
GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSL
KVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRL
MMSKENMKLPQPPEGQTY

Sequence of entity 3 (C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p), FASTA

>3VON_3 Ubiquitin-conjugating enzyme E2 N (chains C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p)
GLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEY
PMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLA
NDVAEQWKTNEAQAIETARAWTRLYAMN

Primary citation

Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13. Sato, Y., Yamagata, A., Goto-Ito, S. et al. J Biol Chem (2012) 287:25860-25868. DOI 10.1074/jbc.M112.364752 · PubMed

Other PDB entries of the same protein (UniProt Q96FW1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZFY 1.69 Å, Crystal structure of human Otubain 1
4LDT 1.9 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
4I6L 2.49 Å, Crystal structure of OTUB1 in complex with ubiquitin variant
4DHZ 3.11 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub
4DDG 3.3 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub
4DDI 3.8 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub

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