6ML1: USP15 deubiquitinase domain

Structure of the USP15 deubiquitinase domain in complex with an affinity-matured inhibitory Ubv. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 5
Atoms: 6,889
Mol. weight: 103.8 kDa
Ligands: ZN, CA
Released: 23 Jan 2019

Explore 6ML1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ML1 contains 35 α-helices and 56 β-strands across 5 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	290-291	2	1
α-helix	300-308	9
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-349	13
β-strand	356-357	2	1
α-helix	360-369	10
α-helix	384-395	12
α-helix	402-404	3
α-helix	415-429	15
α-helix	433-438	6
β-strand	440-447	8	2
β-strand	454-461	8	2
β-strand	464-466	3	3
β-strand	785-787	3	4
α-helix	788-795	8
β-strand	799-800	2	2
β-strand	807-809	3	5
β-strand	814-816	3	5
β-strand	819-826	8	2
β-strand	827	1	6
β-strand	830-835	6	3
α-helix	841-843	3
α-helix	846-848	3
β-strand	851-853	3	4
β-strand	859-861	3	3
β-strand	873-884	12	3
β-strand	891-897	7	3
β-strand	904-908	5	3
β-strand	911-914	4	3
α-helix	917-919	3
β-strand	925-932	8	3

Chain B: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	290-291	2	7
α-helix	300-308	9
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-349	13
β-strand	356-357	2	7
α-helix	360-369	10
α-helix	383-395	13
α-helix	402-404	3
α-helix	415-429	15
α-helix	433-438	6
β-strand	440-447	8	8
β-strand	454-461	8	8
β-strand	464-467	4	9
β-strand	785-787	3	10
α-helix	788-795	8
β-strand	799-800	2	8
α-helix	801-802	2
β-strand	807-809	3	11
β-strand	814-816	3	11
β-strand	819-826	8	8
β-strand	830-836	7	9
α-helix	842-844	3
β-strand	851-853	3	10
β-strand	859-861	3	9
β-strand	873-884	12	9
β-strand	891-897	7	9
β-strand	904-908	5	9
β-strand	911-914	4	9
α-helix	917-919	3
β-strand	925-932	8	9

Chain C: 4 helices, 9 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	41-45	5	15
β-strand	55-56	2	15
α-helix	57-58	2
β-strand	62	1	16
α-helix	63-66	4
β-strand	73-78	6	15
β-strand	79-80	2	17
β-strand	83-84	2	17

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	12
β-strand	12-17	6	12
β-strand	22	1	13
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	12
β-strand	55-56	2	12
α-helix	57-58	2
β-strand	62	1	13
α-helix	64-66	3
α-helix	68-69	2
β-strand	73-78	6	12
β-strand	80	1	14
β-strand	83	1	14

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin…	A, B	protein	349	Homo sapiens	Q9Y4E8 (AlphaFold model)
Ubiquitin variant 15.1a	C, E	protein	92	Homo sapiens	A0A0L7RG06 (AlphaFold model)
Proteolyzed N-terminal tag of Ubv.15.1a construct	G	protein	26	Escherichia coli

Sequence of entity 1 (A, B), FASTA

>6ML1_1 Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B)
SGAAADYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFD
NPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLL
DGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP
ECAKISVTFDPFCYLTLPLPMPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQAT
KKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSGCRYNLIAVSNHYGGMG
GGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDSSG

Sequence of entity 2 (C, E), FASTA

>6ML1_2 Ubiquitin variant 15.1a (chains C, E)
GAAMLIFVKTLSGKFISLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKRLSFYRKQL
EDGRTLSDYNIQKHSTLQLLVISRGILYGSSG

Sequence of entity 3 (G), FASTA

>6ML1_3 Proteolyzed N-terminal tag of Ubv.15.1a construct (chains G)
MAHHHHHHDTSLYKKAGSTENLYFQG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	4

Water and common crystallization additives (NA, MES, CL, EDO) 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
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
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

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