3C0R: Ovarian Tumor (OTU) domain

Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin. Determined by X-ray diffraction at 2.31 Å resolution. Released 19 Feb 2008.

Method: X-ray diffraction
Resolution: 2.31 Å
Organisms: Saccharomyces cerevisiae, Homo sapiens
Chains: 4
Atoms: 4,296
Mol. weight: 65.46 kDa
Ligands: 3CN
Released: 19 Feb 2008

Explore 3C0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C0R contains 20 α-helices and 30 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	98-100	3	1
β-strand	108-112	5	1
α-helix	120-130	11
α-helix	135-147	13
α-helix	155-158	4
α-helix	162-168	7
α-helix	174-176	3
α-helix	178-188	11
β-strand	191-196	6	1
β-strand	201-205	5	1
β-strand	212-218	7	1
β-strand	223-228	6	1
β-strand	232	1	1
β-strand	235-236	2	1
α-helix	240-258	19

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	2
β-strand	12-14	3	2
β-strand	22	1	3
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	2
β-strand	48-49	2	2
β-strand	55	1	3
α-helix	57-59	3
α-helix	65	1
β-strand	66-71	6	2

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	98-101	4	4
β-strand	107-112	6	4
α-helix	120-130	11
α-helix	136-148	13
α-helix	155-158	4
α-helix	162-168	7
α-helix	175-176	2
α-helix	178-188	11
β-strand	191-196	6	4
β-strand	201-205	5	4
β-strand	212-218	7	4
β-strand	223-228	6	4
β-strand	232	1	4
β-strand	235-236	2	4
α-helix	240-258	19

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
β-strand	55	1	6
β-strand	66-71	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase OTU1	A, C	protein	212	Saccharomyces cerevisiae	P43558 (AlphaFold model)
Ubiquitin	B, D	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3C0R_1 Ubiquitin thioesterase OTU1 (chains A, C)
MKRVLKSTEMSIGGSGENVLSVHPVLDDNSCLFHAIAYGIFKQDSVRDLREMVSKEVLNN
PVKFNDAILDKPNKDYAQWILKMESWGGAIEIGIISDALAVAIYVVDIDAVKIEKFNEDK
FDNYILILFNGIHYDSLTMNEFKTVFNKNQPESDDVLTAALQLASNLKQTGYSFNTHKAQ
IKCNTCQMTFVGEREVARHAESTGHVDFGQNR

Sequence of entity 2 (B, D), FASTA

>3C0R_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
3CN	3-aminopropane	C3 H9 N	2

Primary citation

Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. Messick, T.E., Russell, N.S., Iwata, A.J. et al. J Biol Chem (2008) 283:11038-11049. DOI 10.1074/jbc.M704398200 · PubMed

Other PDB entries of the same protein (UniProt P43558 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BY4 1.55 Å, Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin
4KDL 1.81 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
4KDI 1.86 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL

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