8D1T: Human USP30

Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab. Determined by X-ray diffraction at 2.94 Å resolution. Released 1 Feb 2023.

Method: X-ray diffraction
Resolution: 2.94 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 5,608
Mol. weight: 88.21 kDa
Ligands: PXW, ZN
Released: 1 Feb 2023

Explore 8D1T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D1T contains 24 α-helices and 54 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: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-86	10
α-helix	90-99	10
α-helix	110-113	4
α-helix	115-126	12
β-strand	137-138	2	1
α-helix	141-147	7
α-helix	157-159	3
α-helix	162-178	17
α-helix	220-222	3
β-strand	226-234	9	2
β-strand	240	1	2
α-helix	241-243	3
β-strand	244-248	5	2
β-strand	251-253	3	3
α-helix	256-258	3
α-helix	262-263	2
β-strand	264-265	2	4
α-helix	266-274	9
β-strand	278-282	5	2
β-strand	306-316	11	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
α-helix	352-354	3
β-strand	355	1	2
β-strand	435-445	11	3
β-strand	452-458	7	3
α-helix	459-462	4
β-strand	473-477	5	3
β-strand	480-484	5	3
α-helix	486-490	5
β-strand	494-502	9	3

Chain H: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	10-12	3	7
β-strand	17-24	8	6
α-helix	29-31	3
β-strand	34-40	7	7
β-strand	44-51	8	7
β-strand	58-60	3	7
β-strand	68-73	6	6
β-strand	78-84	7	6
α-helix	88-90	3
β-strand	92-98	7	7
α-helix	104-105	2
β-strand	106-107	2	7
α-helix	108-110	3
β-strand	111-115	5	7
β-strand	121	1	8
β-strand	124-127	4	9
β-strand	143-149	7	9
β-strand	150	1	8
β-strand	168-174	7	9
β-strand	179-184	6	9

Chain L: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	10
β-strand	10-13	4	11
β-strand	18-25	8	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-76	7	10
β-strand	85-90	6	11
β-strand	98	1	11
β-strand	102-106	5	11
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	12
β-strand	144	1	13
β-strand	159-163	5	12
α-helix	164-166	3
β-strand	173-182	10	12
α-helix	183-188	6
β-strand	198	1	13

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

>8D1T_1 Ubiquitin carboxyl-terminal hydrolase 30 (chains A)
MKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLLH
LLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSGS
HWKSQHPFHGRLTSNMVCKHCEHQSPVRFDTFDSLSLSIPAATWGHPLTLDHCLHHFISS
ESVRDVVCDNCTKIEAKGTLNGEKVEHQRTTFVKQLKLGKLPQCLCIHLQRLSWSSHGTP
LKRHEHVQFNEDLSMDEYKYHSNASTYLFRLMAVVVHHGDMHSGHFVTYRRSPPSARNPL
STSNQWLWVSDDTVRKASLQEVLSSSAYLLFYERVLEVLFQGPHHHHHH

Sequence of entity 2 (H), FASTA

>8D1T_2 mouse anti-huUSP30 Fab heavy chain (chains H)
EVQLQQSGAELVRPGASVKLSCTGSGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKY
DPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCARPDGYYGDYWGQGTTLTVSSAKT
TAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIGGHHHHHH

Sequence of entity 3 (L), FASTA

>8D1T_3 mouse anti-huUSP30 Fab light chain (chains L)
DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPD
RFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSFPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
PXW	(1R,2R,4S,7E)-7-[amino(sulfanyl)methylidene]-2-{[(1P)-3-chloro-3'-(1-cyanocyclo…	C24 H24 Cl N4 O S	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

TBD. Song, X., Butler, J., Li, C. et al. 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
8D0A 3.19 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 829 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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