8D0A: Human USP30

Crystal structure of human USP30 in complex with a covalent inhibitor 829 and a Fab. Determined by X-ray diffraction at 3.19 Å resolution. Released 1 Feb 2023.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,489
Mol. weight: 88.13 kDa
Ligands: ZN, PKH
Released: 1 Feb 2023

Explore 8D0A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D0A contains 26 α-helices and 55 β-strands across 3 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: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-86	10
α-helix	90-101	12
α-helix	110-113	4
α-helix	115-128	14
α-helix	130-131	2
β-strand	137-138	2	1
α-helix	141-148	8
α-helix	157-159	3
α-helix	162-177	16
α-helix	220-222	3
β-strand	226-234	9	2
β-strand	239-240	2	2
α-helix	241-243	3
β-strand	244-248	5	2
β-strand	251-253	3	3
α-helix	254-258	5
α-helix	262-263	2
β-strand	264-265	2	4
α-helix	266-273	8
β-strand	278-279	2	2
β-strand	308-316	9	2
β-strand	320-325	6	3
β-strand	328-330	3	5
β-strand	336-338	3	5
β-strand	343-344	2	4
β-strand	348-350	3	3
β-strand	355	1	2
β-strand	435-445	11	3
α-helix	448-450	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	486-491	6
β-strand	494-502	9	3

Chain H: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
α-helix	7-9	3
β-strand	11-12	2	7
β-strand	17-24	8	6
β-strand	34-40	7	8
β-strand	44-51	8	8
β-strand	59-60	2	8
β-strand	68-72	5	6
β-strand	79-84	6	6
α-helix	88-90	3
β-strand	92-98	7	8
α-helix	104-105	2
β-strand	106-107	2	8
α-helix	108-110	3
β-strand	111-113	3	8
β-strand	114-115	2	7
β-strand	125-128	4	9
β-strand	143-146	4	9
β-strand	168-169	2	9
α-helix	170-172	3
β-strand	173-175	3	10
β-strand	178-180	3	10
β-strand	181-184	4	9

Chain L: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	10-13	4	12
β-strand	18-25	8	11
β-strand	33-38	6	12
α-helix	43-44	2
β-strand	45-48	4	12
β-strand	54	1	12
β-strand	62-67	6	11
β-strand	70-76	7	11
β-strand	85-90	6	12
α-helix	96	1
β-strand	98	1	12
β-strand	102-106	5	12
β-strand	114-118	5	13
α-helix	122-126	5
β-strand	129-137	9	13
β-strand	145	1	14
β-strand	160-163	4	13
α-helix	164-166	3
β-strand	174-182	9	13
α-helix	183-186	4
β-strand	197	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30	A	protein	349	Homo sapiens	Q70CQ3 (AlphaFold model)
mouse anti-huUSP30 Fab heavy chain	H	protein	222	Mus musculus
mouse anti-huUSP30 Fab light chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>8D0A_1 Ubiquitin carboxyl-terminal hydrolase 30 (chains A)
MKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLLH
LLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSGS
HWKSQHPFHGRLTSNMVCKHCEHQSPVRFDTFDSLSLSIPAATWGHPLTLDHCLHHFISS
ESVRDVVCDNCTKIEAKGTLNGEKVEHQRTTFVKQLKLGKLPQCLCIHLQRLSWSSHGTP
LKRHEHVQFNEDLSMDEYKYHSNASTYLFRLMAVVVHHGDMHSGHFVTYRRSPPSARNPL
STSNQWLWVSDDTVRKASLQEVLSSSAYLLFYERVLEVLFQGPHHHHHH

Sequence of entity 2 (H), FASTA

>8D0A_2 mouse anti-huUSP30 Fab heavy chain (chains H)
EVQLQQSGAELVRPGASVKLSCTGSGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKY
DPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCARPDGYYGDYWGQGTTLTVSSAKT
TAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIGGHHHHHH

Sequence of entity 3 (L), FASTA

>8D0A_3 mouse anti-huUSP30 Fab light chain (chains L)
DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPD
RFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSFPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PKH	~{N}-[(1~{R},2~{R},4~{S},7~{E})-7-[azanyl(sulfanyl)methylidene]-7$l^{4}-azabicy…	C21 H23 Cl N5 O S	1

Primary citation

TBD. Song, X., Butler, J., Hao, Y. To be published.

Other PDB entries of the same protein (UniProt Q70CQ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
5OHK 2.34 Å, Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high…
9LYF 2.58 Å, Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30
9F19 2.75 Å, Human USP30 chimera in complex with NK036 inhibitor
5OHP 2.8 Å, Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
8D1T 2.94 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab
5OHN 3.6 Å, Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low…

Browse structure collections

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