9F6G: Human USP30 chimera

Human USP30 chimera bound to Ubiquitin-PA. Determined by X-ray diffraction at 1.5 Å resolution. Released 19 Mar 2025.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,126
Mol. weight: 44.7 kDa
Ligands: AYE
Released: 19 Mar 2025

Explore 9F6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F6G contains 15 α-helices and 25 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-86	10
α-helix	90-99	10
α-helix	117-127	11
β-strand	137-138	2	1
α-helix	141-150	10
α-helix	162-174	13
β-strand	226-234	9	2
α-helix	241-242	2
β-strand	243-249	7	2
β-strand	252-254	3	3
α-helix	255-258	4
β-strand	265	1	4
α-helix	266-274	9
β-strand	277-283	7	2
β-strand	288-300	13	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	348-352	5	3
α-helix	354-356	3
β-strand	358-446	14	3
β-strand	451-458	8	3
α-helix	459-462	4
β-strand	473-477	5	3
β-strand	480-484	5	3
α-helix	486-491	6
β-strand	494-501	8	3

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	6
β-strand	48-49	2	6
α-helix	50	1
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-70	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin…	A	protein	317	Homo sapiens	P54578 (AlphaFold model), Q70CQ3 (AlphaFold model), Q9P2H5 (AlphaFold model)
Polyubiquitin-B	B	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9F6G_1 Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35 (chains A)
GPKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLL
HLLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSG
SHWKSQHPFGVEFETTMKCTESEEEEVTKGKENQDSLSLSIPAATWGHPLTLDHCLHHFI
SQEEITKQSPTLQRNALYIKSSKISRLPQCLCIHLQRLSWSSHGTPLKRHEHVQFNEDLR
LPLAGGRGQAYRLMAVVVHHGDMHSGHFVTYRRSPPSARNPLSTSNQWLWVSDDTVRKAS
LQEVLSSSAYLLFYERV

Sequence of entity 2 (B), FASTA

>9F6G_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
AYE	prop-2-en-1-amine	C3 H7 N	1

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:

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
9F19 2.75 Å, Human USP30 chimera in complex with NK036 inhibitor
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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