4DHI: C. elegans OTUB1

Structure of C. elegans OTUB1 bound to human UBC13. Determined by X-ray diffraction at 1.8 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Caenorhabditis elegans, Homo sapiens
Chains: 2
Atoms: 3,528
Mol. weight: 49.48 kDa
Released: 22 Feb 2012

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

Secondary structure: helices and β-sheets

4DHI contains 21 α-helices and 14 β-strands across 2 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 B: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	44	1	1
α-helix	45-47	3
β-strand	48-49	2	2
α-helix	50-55	6
α-helix	63-73	11
β-strand	76-80	5	2
β-strand	82	1	1
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	215-224	10
β-strand	229-233	5	2
α-helix	236-238	3
β-strand	245-248	4	2
β-strand	259-264	6	2
β-strand	267-273	7	2

Chain D: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	3
β-strand	34-40	7	3
α-helix	41-42	2
β-strand	51-57	7	3
α-helix	66-67	2
β-strand	68-71	4	3
β-strand	80	1	4
β-strand	86	1	4
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase otubain-like	B	protein	284	Caenorhabditis elegans	Q9XVR6 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	D	protein	152	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>4DHI_1 Ubiquitin thioesterase otubain-like (chains B)
MANEPQKSDDNGQAAEAVVTDDEIVLQDQQLKTIEDEQKSVPLVATLAPFSILCAEYDNE
TSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSRDWTR
TLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLITSAF
LKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDRTAAP
NGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYKKDSTEASEIEN

Sequence of entity 2 (D), FASTA

>4DHI_2 Ubiquitin-conjugating enzyme E2 N (chains D)
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:

4LDT 1.9 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub
4DHJ 2.35 Å, The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex
4DHZ 3.11 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub

Browse structure collections

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