9F19: Human USP30 chimera

Human USP30 chimera in complex with NK036 inhibitor. Determined by X-ray diffraction at 2.75 Å resolution. Released 19 Mar 2025.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,932
Mol. weight: 73.28 kDa
Ligands: A1H8X
Released: 19 Mar 2025

Explore 9F19 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F19 contains 22 α-helices and 34 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-87	11
α-helix	90-98	9
α-helix	116-127	12
β-strand	137-138	2	1
α-helix	141-149	9
α-helix	154-156	3
α-helix	163-177	15
β-strand	226-233	8	2
β-strand	241-248	8	2
β-strand	251-253	3	3
α-helix	256-259	4
β-strand	265	1	4
α-helix	266-275	10
β-strand	295-300	6	2
β-strand	320-325	6	3
β-strand	328-330	3	5
β-strand	336-338	3	5
β-strand	344	1	4
β-strand	348-350	3	3
α-helix	351-352	2
β-strand	360-445	11	3
β-strand	452-458	7	3
α-helix	459-460	2
β-strand	473-477	5	3
β-strand	480-484	5	3
α-helix	486-490	5
β-strand	494-501	8	3

Chain B: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	6
α-helix	77-86	10
α-helix	90-99	10
α-helix	100-102	3
α-helix	116-127	12
β-strand	137-138	2	6
α-helix	141-149	9
α-helix	155-159	5
α-helix	163-177	15
β-strand	226-227	2	7
β-strand	247-248	2	7
β-strand	251-254	4	8
β-strand	264-265	2	9
α-helix	266-272	7
β-strand	300	1	7
β-strand	320-326	7	8
β-strand	328-329	2	10
β-strand	337-338	2	10
β-strand	343-344	2	9
β-strand	348-351	4	8
α-helix	355-357	3
β-strand	359-444	11	8
β-strand	453-458	6	8
α-helix	459-462	4
β-strand	473-477	5	8
β-strand	480-484	5	8
α-helix	486-491	6
β-strand	494-501	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin…	A, B	protein	317	Homo sapiens	P54578 (AlphaFold model), Q70CQ3 (AlphaFold model), Q9P2H5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9F19_1 Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35 (chains A, B)
GPKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLL
HLLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSG
SHWKSQHPFGVEFETTMKCTESEEEEVTKGKENQDSLSLSIPAATWGHPLTLDHCLHHFI
SQEEITKQSPTLQRNALYIKSSKISRLPQCLCIHLQRLSWSSHGTPLKRHEHVQFNEDLR
LPLAGGRGQAYRLMAVVVHHGDMHSGHFVTYRRSPPSARNPLSTSNQWLWVSDDTVRKAS
LQEVLSSSAYLLFYERV

Ligands and cofactors

ID	Name	Formula	Copies
A1H8X	4-fluoranyl-~{N}-[(2~{S})-1-[[4-[(2-methyl-1-oxidanyl-propan-2-yl)sulfamoyl]phe…	C26 H28 F N3 O5 S	2

Primary citation

Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30. Kazi, N.H., Klink, N., Gallant, K. et al. Nat Struct Mol Biol (2025) 32:1776-1786. DOI 10.1038/s41594-025-01534-4 · PubMed

Other PDB entries of the same protein (UniProt P54578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
6IIK 1.97 Å, USP14 catalytic domain with IU1
6IIL 2.2 Å, USP14 catalytic domain bind to IU1-47
6IIM 2.21 Å, USP14 catalytic domain with IU1-206
6IIN 2.53 Å, USP14 catalytic domain with IU1-248
6LVS 2.73 Å, USP14 catalytic domain mutant C114S
7W37 3.0 Å, Structure of USP14-bound human 26S proteasome in state EA1_UBL
7W38 3.1 Å, Structure of USP14-bound human 26S proteasome in state EA2.0_UBL
2AYN 3.2 Å, Structure of USP14, a proteasome-associated deubiquitinating enzyme
7W39 3.2 Å, Structure of USP14-bound human 26S proteasome in state EA2.1_UBL
7W3G 3.2 Å, Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14
7W3H 3.2 Å, Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14

Browse structure collections

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