6CPM: USP15 deubiquitinase domain

Structure of the USP15 deubiquitinase domain in complex with a third-generation inhibitory Ubv. Determined by X-ray diffraction at 2.01 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,253
Mol. weight: 99.52 kDa
Ligands: ZN, CA
Released: 23 Jan 2019

Explore 6CPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CPM contains 38 α-helices and 54 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 C: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	281	1	1
β-strand	290-291	2	2
α-helix	298-308	11
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-349	13
β-strand	354	1	1
β-strand	356-357	2	2
α-helix	360-369	10
α-helix	381-395	15
α-helix	402-404	3
α-helix	415-429	15
α-helix	433-438	6
β-strand	440-447	8	3
β-strand	454-461	8	3
β-strand	464-466	3	4
β-strand	475-477	3	5
α-helix	478-485	8
β-strand	489-490	2	3
α-helix	491-492	2
β-strand	497-499	3	6
β-strand	504-506	3	6
β-strand	509-516	8	3
β-strand	520-525	6	4
α-helix	532-534	3
β-strand	541-543	3	5
β-strand	549-551	3	4
β-strand	554-565	12	4
β-strand	572-578	7	4
β-strand	585-589	5	4
β-strand	592-595	4	4
α-helix	598-600	3
β-strand	606-613	8	4

Chain D: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	281	1	7
β-strand	290-291	2	8
α-helix	298-308	11
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-349	13
β-strand	354	1	7
β-strand	356-357	2	8
α-helix	360-369	10
α-helix	371-373	3
α-helix	381-395	15
α-helix	402-404	3
α-helix	415-429	15
α-helix	433-438	6
β-strand	440-447	8	9
β-strand	454-461	8	9
β-strand	464-466	3	10
α-helix	472-473	2
β-strand	475-477	3	11
α-helix	478-485	8
β-strand	489-490	2	9
α-helix	491-492	2
β-strand	497-499	3	12
β-strand	504-506	3	12
β-strand	509-516	8	9
β-strand	520-525	6	10
α-helix	532-534	3
β-strand	541-543	3	11
β-strand	549-551	3	10
β-strand	554-565	12	10
β-strand	572-578	7	10
β-strand	585-589	5	10
β-strand	592-595	4	10
α-helix	598-600	3
β-strand	606-613	8	10

Chain E: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	13
α-helix	11	1
β-strand	12-17	6	13
β-strand	22	1	14
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-47	7	13
β-strand	50-53	4	13
α-helix	54	1
β-strand	59	1	14
α-helix	61-63	3
α-helix	65-66	2
β-strand	70-75	6	13

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	15
β-strand	12-17	6	15
β-strand	22	1	16
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-47	7	15
β-strand	50-53	4	15
α-helix	54	1
β-strand	59	1	16
α-helix	61-63	3
β-strand	70-75	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15	C, D	protein	349	Homo sapiens	Q9Y4E8 (AlphaFold model)
Ubiquitin variant 15.1d	E, F	protein	86	Homo sapiens

Sequence of entity 1 (C, D), FASTA

>6CPM_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains C, D)
SGAAADYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFD
NPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLL
DGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP
ECAKISVTFDPFCYLTLPLPMPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQAT
KKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSGCRYNLIAVSNHYGGMG
GGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDSSG

Sequence of entity 2 (E, F), FASTA

>6CPM_2 Ubiquitin variant 15.1d (chains E, F)
GAAAMQIFVKTPTGKFISLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFRQTWASKQLED
GRTLSDYNIQKESTLHLVLRLRGSSG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	5

Water and common crystallization additives (EDO, GOL, NA) are not listed.

Primary citation

Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Teyra, J., Singer, A.U., Schmitges, F.W. et al. Structure (2019) 27:590. DOI 10.1016/j.str.2019.01.002 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4E8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4A3P 1.4 Å, Structure of USP15 DUSP-UBL deletion mutant
3T9L 1.5 Å, Structure of N-terminal DUSP-UBL domains of human USP15
6ML1 1.9 Å, Structure of the USP15 deubiquitinase domain in complex with an affinity-matured…
6GHA 1.98 Å, USP15 catalytic domain structure
7R2G 1.98 Å, USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
6GH9 2.09 Å, USP15 catalytic domain in complex with small molecule
3LMN 2.15 Å, Oligomeric structure of the DUSP domain of human USP15
4A3O 2.2 Å, Crystal structure of the USP15 DUSP-UBL monomer
9VVV 2.3 Å, Crystal structure of USP15 catalytic domain in complex with Ub-PA
3PPA 2.35 Å, Structure of the Dusp-Ubl domains of Usp15
6CRN 2.5 Å, Structure of the USP15 deubiquitinase domain in complex with a high-affinity…
3PV1 2.6 Å, Crystal structure of the USP15 DUSP-UBL domains

Browse structure collections

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