5GVI: Zebrafish USP30

Zebrafish USP30 in complex with Lys6-linked diubiquitin. Determined by X-ray diffraction at 1.87 Å resolution. Released 13 Sept 2017.

Method: X-ray diffraction
Resolution: 1.87 Å
Organisms: Danio rerio, Mus musculus
Chains: 3
Atoms: 3,904
Mol. weight: 67.36 kDa
Ligands: ZN
Released: 13 Sept 2017

Explore 5GVI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GVI contains 25 α-helices and 39 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: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	1
α-helix	73-82	10
α-helix	86-95	10
α-helix	111-122	12
β-strand	133-134	2	1
α-helix	137-142	6
α-helix	143-147	5
β-strand	156	1	2
α-helix	158-173	16
α-helix	216-218	3
β-strand	222-230	9	3
α-helix	235	1
β-strand	236	1	3
α-helix	237-239	3
β-strand	240-244	5	3
β-strand	247-250	4	4
α-helix	251-252	2
β-strand	260-261	2	5
α-helix	262-270	9
β-strand	273-279	7	3
α-helix	281-285	5
β-strand	290-291	2	6
β-strand	295-296	2	6
α-helix	298-300	3
β-strand	301-312	12	3
α-helix	313-314	2
β-strand	316-322	7	4
β-strand	324-326	3	7
β-strand	332-334	3	7
β-strand	339-340	2	5
β-strand	344-346	3	4
α-helix	348-350	3
β-strand	379-380	2	3
β-strand	383-384	2	3
β-strand	425-436	12	4
β-strand	441-448	8	4
α-helix	449-452	4
β-strand	463-467	5	4
β-strand	470-474	5	4
α-helix	476-480	5
β-strand	484-491	8	4
α-helix	492-494	3

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	8
β-strand	48-49	2	8
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-70	5	8
β-strand	75	1	2

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	10
β-strand	48-49	2	10
β-strand	55	1	11
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30	A	protein	444	Danio rerio	A2BGT0 (AlphaFold model)
ubiquitin	B	protein	76	Mus musculus	Q78XY9 (AlphaFold model)
ubiquitin	C	protein	72	Mus musculus	Q78XY9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GVI_1 Ubiquitin carboxyl-terminal hydrolase 30 (chains A)
SHMGMVPGLLNLGNTAFMNSLLQGLAACPSFIRWLEDFTSQNSADRERTERETQLSRSLM
QLLKALSSHVPGEDDVLDAGGLLEALRLYRWHISSFEEQDAHELFHVLTSSLEEEQERQP
RVAHLFDMQTLEKSVESKEKNISCRSGGPLHPIPSLWRTRHPFHGRLTSYMACKRCEQQS
PVHYDSFDSLSLSIPSIQWGRPVTLDQCLQHFISSETIKEVECENCTKQQAGELVNGEVL
ESQRTTFVKQLKLGKLPQCLCIHLQRLTWSKEGSPIKRQEHVQFTEYLSLDRYKHCSAAQ
SQQKTSRTNKAKASADPKDKAIANGVDSEHCNNNKPQSNGTFPSVFLHSPGLSSQLNLTY
DYSTSEYLFRLTAVLVHHGDMHSGHFITYRRCPAAPRGTSPFSSQWLWVSDDSVRKASLQ
EVLSSSAYLLFYERMQRPGLRVEE

Sequence of entity 2 (B), FASTA

>5GVI_2 ubiquitin (chains B)
MQIFVRTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>5GVI_3 ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30. Sato, Y., Okatsu, K., Saeki, Y. et al. Nat Struct Mol Biol (2017) 24:911-919. DOI 10.1038/nsmb.3469 · PubMed

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