4DHZ: H/ceOTUB1-ubiquitin aldehyde-UBC13~Ub

The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub. Determined by X-ray diffraction at 3.11 Å resolution. Released 22 Feb 2012.

Method: X-ray diffraction
Resolution: 3.11 Å
Organisms: Homo sapiens, Caenorhabditis elegans
Chains: 4
Atoms: 4,370
Mol. weight: 67.14 kDa
Released: 22 Feb 2012

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

Secondary structure: helices and β-sheets

4DHZ contains 29 α-helices and 36 β-strands across 4 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: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	23-27	5
α-helix	29-40	12
β-strand	44	1	1
α-helix	45-47	3
β-strand	48-49	2	2
α-helix	51-54	4
α-helix	63-75	13
β-strand	76-80	5	2
β-strand	82	1	1
α-helix	88-101	14
α-helix	105-124	20
α-helix	129-148	20
α-helix	153-159	7
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
β-strand	213	1	3
α-helix	215-225	11
β-strand	229-233	5	2
β-strand	244-248	5	2
α-helix	255-257	3
β-strand	259-264	6	2
β-strand	266	1	3
β-strand	267-273	7	2

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	502-507	6	4
β-strand	511-516	6	4
β-strand	522	1	5
α-helix	523-533	11
α-helix	538-540	3
β-strand	541-545	5	4
β-strand	548-549	2	4
β-strand	555	1	5
α-helix	556-559	4
α-helix	561-562	2
β-strand	566-571	6	4
β-strand	575	1	3

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	502-506	5	6
β-strand	512-516	5	6
β-strand	522	1	7
α-helix	524-533	10
β-strand	541-544	4	6
β-strand	549	1	6
β-strand	555	1	7
α-helix	557-559	3
β-strand	566-571	6	6

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	20	1	8
β-strand	23-27	5	8
β-strand	34-40	7	8
α-helix	41-42	2
β-strand	51-57	7	8
α-helix	66-67	2
β-strand	68-71	4	8
β-strand	77	1	9
β-strand	80	1	9
β-strand	85	1	8
β-strand	86	1	9
α-helix	89-91	3
α-helix	101-109	9
β-strand	112	1	10
β-strand	115	1	10
α-helix	124-131	8
α-helix	133-147	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase otubain-like	A	protein	288	Homo sapiens, Caenorhabditis elegans	Q96FW1 (AlphaFold model), Q9XVR6 (AlphaFold model)
Ubiquitin aldehyde	B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin	E	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	F	protein	152	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DHZ_1 Ubiquitin thioesterase otubain-like (chains A)
MAAEEPQQQKQEPLGSDSEGVNCLAYDEAIMAQQDRIQQEIAVQNPLVATLAPFSILCAE
YDNETSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSR
DWTRTLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLI
TSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDR
TAAPNGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYKKDSTEASEIEN

Sequence of entity 2 (B), FASTA

>4DHZ_2 Ubiquitin aldehyde (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (E), FASTA

>4DHZ_3 Ubiquitin (chains E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 4 (F), FASTA

>4DHZ_4 Ubiquitin-conjugating enzyme E2 N (chains F)
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 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
3VON 3.15 Å, Crystalstructure of the ubiquitin protease
4DDG 3.3 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub
4DDI 3.8 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Browse structure collections

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