7R2G: USP15 D1D2 in catalytically-competent state

USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2). Determined by X-ray diffraction at 1.98 Å resolution. Released 8 Jun 2022.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,126
Mol. weight: 88.62 kDa
Ligands: MIX, ZN
Released: 8 Jun 2022

Explore 7R2G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R2G contains 29 α-helices and 40 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 A: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	1
α-helix	269-279	11
α-helix	282-289	8
α-helix	294-296	3
α-helix	308-320	13
β-strand	327-328	2	1
α-helix	331-340	10
α-helix	352-366	15
α-helix	373-375	3
α-helix	386-400	15
α-helix	404-409	6
β-strand	411-418	8	2
β-strand	425-432	8	2
β-strand	435-438	4	3
α-helix	439	1
β-strand	756-758	3	4
α-helix	759-766	8
β-strand	770-771	2	2
β-strand	778-780	3	5
β-strand	785-787	3	5
β-strand	790-797	8	2
β-strand	801-807	7	3
β-strand	822-824	3	4
β-strand	830-831	2	3
α-helix	833-835	3
β-strand	836	1	2
β-strand	845-855	11	3
β-strand	862-868	7	3
β-strand	875-879	5	3
β-strand	882-885	4	3
α-helix	888-890	3
β-strand	896-903	8	3
α-helix	904-906	3
α-helix	914-923	10

Chain B: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	261-262	2	6
α-helix	269-279	11
α-helix	282-289	8
α-helix	294-296	3
α-helix	308-320	13
β-strand	327-328	2	6
α-helix	331-340	10
α-helix	342-344	3
α-helix	352-366	15
α-helix	373-375	3
α-helix	386-400	15
α-helix	404-409	6
β-strand	411-418	8	7
β-strand	425-432	8	7
β-strand	435-437	3	8
β-strand	756-758	3	9
α-helix	759-766	8
β-strand	770-771	2	7
β-strand	778-780	3	10
β-strand	785-787	3	10
β-strand	790-797	8	7
β-strand	801-806	6	8
β-strand	809	1	11
β-strand	818	1	11
β-strand	822-824	3	9
β-strand	830-831	2	8
β-strand	836	1	7
β-strand	845-855	11	8
β-strand	862-868	7	8
β-strand	875-879	5	8
β-strand	882-885	4	8
α-helix	888-890	3
β-strand	896-903	8	8
α-helix	904-906	3
α-helix	914-923	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15	A, B	protein	362	Homo sapiens	Q9Y4E8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7R2G_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B)
MEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSY
AELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKK
PYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFC
YLTLPLASTSKVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVH
LKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTA
FAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDTFSGTGFFPLDRETLEHHHH
HH

Ligands and cofactors

ID	Name	Formula	Copies
MIX	1,4-dihydroxy-5,8-BIS({2-[(2-hydroxyethyl)amino]ethyl}amino)-9,10-anthracenedio…	C22 H28 N4 O6	12
ZN	Zinc ion	Zn	2

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

Primary citation

Mitoxantrone stacking does not define the active or inactive state of USP15 catalytic domain. Priyanka, A., Tisi, D., Sixma, T.K. J Struct Biol (2022) 214:107862-107862. DOI 10.1016/j.jsb.2022.107862 · 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
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
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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