9VVV: USP15 catalytic domain

Crystal structure of USP15 catalytic domain in complex with Ub-PA. Determined by X-ray diffraction at 2.3 Å resolution. Released 24 Jun 2026.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,704
Mol. weight: 96.44 kDa
Ligands: ZN
Released: 24 Jun 2026

Explore 9VVV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VVV contains 29 α-helices and 56 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: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	290-291	2	1
α-helix	298-308	11
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-351	15
β-strand	356-357	2	1
α-helix	360-369	10
β-strand	380	1	2
α-helix	381-395	15
α-helix	405-407	3
α-helix	415-427	13
α-helix	433-438	6
β-strand	440-447	8	3
β-strand	454-461	8	3
β-strand	463-466	4	4
β-strand	785-787	3	5
α-helix	788-795	8
β-strand	799-800	2	3
β-strand	807-808	2	6
β-strand	815-816	2	6
β-strand	819-826	8	3
β-strand	830-835	6	4
β-strand	838	1	7
β-strand	847	1	7
β-strand	851-853	3	5
β-strand	859-860	2	4
α-helix	862-864	3
β-strand	865	1	3
α-helix	870-872	3
β-strand	874-885	12	4
β-strand	890-897	8	4
β-strand	904-908	5	4
β-strand	911-915	5	4
β-strand	925-932	8	4

Chain B: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	290-291	2	10
α-helix	298-308	11
α-helix	311-318	8
α-helix	322-325	4
α-helix	337-349	13
β-strand	356-357	2	10
α-helix	360-369	10
α-helix	381-395	15
α-helix	415-427	13
α-helix	433-438	6
β-strand	440-447	8	11
β-strand	454-461	8	11
β-strand	463-466	4	12
β-strand	785-787	3	13
α-helix	788-795	8
β-strand	799-800	2	11
β-strand	807-809	3	14
β-strand	814-816	3	14
β-strand	819-826	8	11
β-strand	830-835	6	12
β-strand	851-853	3	13
β-strand	859-860	2	12
α-helix	862-864	3
β-strand	865	1	11
β-strand	874-885	12	12
β-strand	890-897	8	12
β-strand	904-908	5	12
β-strand	911-914	4	12
α-helix	917-919	3
β-strand	925-932	8	12

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	8
β-strand	48-49	2	8
β-strand	55	1	9
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-70	5	8
β-strand	74	1	2

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
β-strand	12-16	5	15
β-strand	22	1	16
α-helix	23-34	12
β-strand	42-45	4	15
β-strand	48-49	2	15
β-strand	55	1	16
α-helix	56-59	4
β-strand	66-70	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15	A, B	protein	347	Homo sapiens	Q9Y4E8 (AlphaFold model)
Polyubiquitin-C	C, D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9VVV_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B)
SEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSY
AELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKK
PYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFC
YLTLPLASTSKVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVH
LKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTA
FAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGF

Sequence of entity 2 (C, D), FASTA

>9VVV_2 Polyubiquitin-C (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (IMD) are not listed.

Primary citation

Structural insights into ubiquitin recognition by USP15 revealed through a covalent activity-based probe. Liu, B., Wang, T., Luo, H. et al. Commun Biol (2026) 9. DOI 10.1038/s42003-026-10386-7 · 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)
6CPM 2.01 Å, Structure of the USP15 deubiquitinase domain in complex with a third-generation…
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
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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