6CRN: USP15 deubiquitinase domain

Structure of the USP15 deubiquitinase domain in complex with a high-affinity first-generation Ubv. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 13,451
Mol. weight: 200.4 kDa
Ligands: ZN
Released: 23 Jan 2019

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

Secondary structure: helices and β-sheets

6CRN contains 72 α-helices and 120 β-strands across 8 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, 25 β-strands

Element	Residues	Length	Sheet
β-strand	281	1	1
β-strand	290-291	2	2
β-strand	297	1	3
β-strand	299	1	3
α-helix	300-308	9
α-helix	311-318	8
α-helix	337-349	13
β-strand	354	1	1
β-strand	356-357	2	2
α-helix	360-369	10
α-helix	371-373	3
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	4
β-strand	454-461	8	4
β-strand	464-466	3	5
α-helix	467-469	3
α-helix	472-473	2
β-strand	475-477	3	6
α-helix	478-485	8
β-strand	489-490	2	4
β-strand	497-499	3	7
β-strand	504-506	3	7
β-strand	509-516	8	4
β-strand	520-525	6	5
β-strand	528-530	3	8
α-helix	531-533	3
β-strand	535-537	3	8
β-strand	541-543	3	6
β-strand	549-550	2	5
α-helix	552-554	3
β-strand	555	1	4
β-strand	564-574	11	5
β-strand	581-587	7	5
β-strand	594-598	5	5
β-strand	601-605	5	5
α-helix	607-609	3
β-strand	615-622	8	5

Chain B: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	290-291	2	9
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	9
α-helix	360-369	10
α-helix	371-373	3
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	10
β-strand	454-461	8	10
β-strand	464-467	4	11
α-helix	468-469	2
α-helix	472-473	2
β-strand	475-477	3	12
α-helix	478-485	8
β-strand	489-490	2	10
β-strand	497-499	3	13
β-strand	504-506	3	13
β-strand	509-516	8	10
β-strand	520-526	7	11
β-strand	528	1	14
β-strand	537	1	14
β-strand	541-543	3	12
β-strand	549-550	2	11
α-helix	552-554	3
β-strand	555	1	10
β-strand	564-574	11	11
β-strand	581-587	7	11
β-strand	594-598	5	11
β-strand	601-605	5	11
α-helix	607-610	4
β-strand	615-622	8	11

Chain C: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	281	1	15
β-strand	290-291	2	16
α-helix	300-308	9
α-helix	311-318	8
α-helix	323-325	3
α-helix	337-349	13
β-strand	354	1	15
β-strand	356-357	2	16
α-helix	360-369	10
α-helix	371-373	3
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	17
β-strand	454-461	8	17
β-strand	464-467	4	18
α-helix	468-469	2
α-helix	472-473	2
β-strand	475-477	3	19
α-helix	478-485	8
β-strand	489-490	2	17
β-strand	497-499	3	20
β-strand	504-506	3	20
α-helix	508	1
β-strand	509-516	8	17
β-strand	520-526	7	18
β-strand	541-543	3	19
β-strand	549-550	2	18
α-helix	552-554	3
β-strand	555	1	17
β-strand	564-574	11	18
β-strand	581-587	7	18
β-strand	594-598	5	18
β-strand	601-605	5	18
α-helix	607-609	3
β-strand	615-622	8	18

Chain D: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	281	1	21
β-strand	290-291	2	22
β-strand	297	1	23
β-strand	299	1	23
α-helix	300-308	9
α-helix	311-318	8
α-helix	337-349	13
β-strand	354	1	21
β-strand	356-357	2	22
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	24
β-strand	454-461	8	24
β-strand	464-466	3	25
α-helix	467-469	3
α-helix	472-473	2
β-strand	475-477	3	26
α-helix	478-485	8
β-strand	489-490	2	24
β-strand	498	1	27
β-strand	505	1	27
β-strand	509-516	8	24
β-strand	520-525	6	25
β-strand	528-530	3	28
β-strand	535-537	3	28
β-strand	541-543	3	26
β-strand	549-550	2	25
α-helix	552-554	3
β-strand	555	1	24
β-strand	564-574	11	25
β-strand	581-587	7	25
β-strand	594-598	5	25
β-strand	601-605	5	25
α-helix	607-609	3
β-strand	615-622	8	25

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	29
β-strand	12-17	6	29
β-strand	22	1	30
α-helix	23-34	12
β-strand	42-45	4	29
β-strand	48-49	2	29
α-helix	50-51	2
β-strand	55	1	30
α-helix	61-62	2
β-strand	66-70	5	29

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	31
β-strand	12-17	6	31
β-strand	22	1	32
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	31
β-strand	48-50	3	31
α-helix	51	1
β-strand	55	1	32
α-helix	61-62	2
β-strand	66-71	6	31

Chain G: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	33
β-strand	12-17	6	33
β-strand	22	1	34
α-helix	23-34	12
β-strand	43-45	3	33
β-strand	48-49	2	33
α-helix	50-51	2
β-strand	55	1	34
α-helix	61-62	2
β-strand	66-69	4	33

Chain H: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	35
β-strand	14-17	4	35
β-strand	22	1	36
α-helix	23-34	12
β-strand	43-45	3	35
β-strand	48-50	3	35
α-helix	51	1
β-strand	55	1	36
α-helix	61-62	2
β-strand	66-69	4	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 15	A, B, C, D	protein	360	Homo sapiens	Q9Y4E8 (AlphaFold model)
Ubiquitin variant 15.2	E, F, G, H	protein	81	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>6CRN_1 Ubiquitin carboxyl-terminal hydrolase 15 (chains A, B, C, D)
SGAAADYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFD
NPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLL
DGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCP
ECAKISVTFDPFCYLTLPLPMPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQAT
KKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSEFLINPNAGPCRYNLIA
VSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDSSGZN

Sequence of entity 2 (E, F, G, H), FASTA

>6CRN_2 Ubiquitin variant 15.2 (chains E, F, G, H)
GAAMQIFVKTLASKFISLEVEPSDTIENVKAKIQDKEGIPPDQQTLIFARKQLEDGRTLS
DYNIQKYSTLHLLLRLRGSSG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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)
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
3PV1 2.6 Å, Crystal structure of the USP15 DUSP-UBL domains

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