4DHJ: CeOTUB1 ubiquitin aldehyde UBC13~Ub complex

The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex. Determined by X-ray diffraction at 2.35 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Caenorhabditis elegans, Homo sapiens
Chains: 14
Atoms: 16,392
Mol. weight: 249.41 kDa
Released: 22 Feb 2012

Explore 4DHJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DHJ contains 110 α-helices and 121 β-strands across 14 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: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	30-37	8
α-helix	38-40	3
β-strand	44	1	1
α-helix	45-47	3
β-strand	48-49	2	2
α-helix	51-54	4
α-helix	63-72	10
β-strand	76-80	5	2
β-strand	82	1	1
α-helix	88-102	15
α-helix	105-124	20
α-helix	129-147	19
α-helix	153-160	8
α-helix	163-183	21
α-helix	185-188	4
α-helix	189-191	3
α-helix	198-201	4
α-helix	202-206	5
α-helix	211-212	2
β-strand	213	1	3
α-helix	215-224	10
β-strand	229-233	5	2
β-strand	245-248	4	2
α-helix	255-257	3
β-strand	259-264	6	2
β-strand	266	1	3
β-strand	267-273	7	2

Chains B, J and M: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	502-507	6	4
β-strand	512-516	5	4
β-strand	522	1	5
α-helix	523-534	12
α-helix	538-540	3
β-strand	541-545	5	4
β-strand	548-549	2	4
α-helix	550-551	2
β-strand	555	1	5
α-helix	557-559	3
β-strand	566-571	6	4
β-strand	575	1	3

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	20	1	13
β-strand	23-27	5	13
β-strand	34-40	7	13
α-helix	41-42	2
β-strand	51-57	7	13
α-helix	66-67	2
β-strand	68-71	4	13
β-strand	73	1	14
β-strand	77	1	15
β-strand	80	1	15
β-strand	85	1	13
β-strand	86	1	15
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	502-506	5	11
β-strand	512-516	5	11
β-strand	522	1	12
α-helix	523-531	9
β-strand	542-545	4	11
β-strand	548-549	2	11
β-strand	555	1	12
α-helix	557-559	3
β-strand	566-570	5	11

Chain E: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
β-strand	44	1	6
α-helix	45-47	3
β-strand	48-49	2	7
α-helix	51-54	4
α-helix	63-72	10
β-strand	76-80	5	7
β-strand	82	1	6
α-helix	88-103	16
α-helix	105-124	20
α-helix	129-148	20
α-helix	153-161	9
α-helix	163-183	21
α-helix	185-188	4
α-helix	189-191	3
α-helix	198-205	8
α-helix	211-212	2
β-strand	213	1	8
α-helix	215-224	10
β-strand	229-233	5	7
β-strand	244-248	5	7
α-helix	256-257	2
β-strand	259-264	6	7
β-strand	266	1	8
β-strand	267-273	7	7

Chain F: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	502-507	6	9
β-strand	512-516	5	9
β-strand	522	1	10
α-helix	523-534	12
α-helix	538-540	3
β-strand	541-545	5	9
β-strand	548-549	2	9
β-strand	555	1	10
β-strand	566-571	6	9
β-strand	575	1	8

Chain G: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	23
β-strand	34-40	7	23
α-helix	41-42	2
β-strand	51-57	7	23
α-helix	66-67	2
β-strand	68-71	4	23
β-strand	77	1	24
β-strand	80	1	24
β-strand	85	1	23
β-strand	86	1	24
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	135-147	13

Chain H: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	502-507	6	30
β-strand	512-516	5	30
β-strand	522	1	31
β-strand	544-545	2	30
β-strand	548-549	2	30
α-helix	550-551	2
β-strand	555	1	31
α-helix	556-558	3
β-strand	566-569	4	30

4 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 otubain-like	A, E, I, L	protein	284	Caenorhabditis elegans	Q9XVR6 (AlphaFold model)
Ubiquitin aldehyde	B, F, J, M	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin	D, H	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	C, G, K, N	protein	152	Homo sapiens	P61088 (AlphaFold model)

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

>4DHJ_1 Ubiquitin thioesterase otubain-like (chains A, E, I, L)
MANEPQKSDDNGQAAEAVVTDDEIVLQDQQLKTIEDEQKSVPLVATLAPFSILCAEYDNE
TSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSRDWTR
TLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLITSAF
LKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAP
NGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYKKDSTEASEIEN

Sequence of entity 2 (B, F, J, M), FASTA

>4DHJ_2 Ubiquitin aldehyde (chains B, F, J, M)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (D, H), FASTA

>4DHJ_3 Ubiquitin (chains D, H)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 4 (C, G, K, N), FASTA

>4DHJ_4 Ubiquitin-conjugating enzyme E2 N (chains C, G, K, N)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Primary citation

The mechanism of OTUB1-mediated inhibition of ubiquitination. Wiener, R., Zhang, X., Wang, T. et al. Nature (2012) 483:618-622. DOI 10.1038/nature10911 · PubMed

Other PDB entries of the same protein (UniProt Q9XVR6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
4LDT 1.9 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
4DHZ 3.11 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub

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