3WXG: CYLD USP domain

Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Feb 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Danio rerio, Mus musculus
Chains: 6
Atoms: 7,218
Mol. weight: 105.55 kDa
Released: 11 Feb 2015

Explore 3WXG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WXG contains 40 α-helices and 70 β-strands across 6 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	584-585	2	1
β-strand	588-589	2	2
α-helix	596-606	11
α-helix	613-616	4
α-helix	628-633	6
α-helix	634-640	7
α-helix	641-646	6
β-strand	648-649	2	2
α-helix	651-664	14
β-strand	675	1	3
α-helix	677-682	6
α-helix	683-688	6
β-strand	695-698	4	4
α-helix	699-701	3
β-strand	704-707	4	4
β-strand	710-711	2	1
β-strand	724	1	5
α-helix	725-735	11
β-strand	740	1	4
β-strand	746-750	5	1
β-strand	753	1	6
β-strand	759	1	6
β-strand	765	1	5
β-strand	769-771	3	1
α-helix	773-775	3
β-strand	776	1	4
β-strand	788-797	10	1
β-strand	802-807	6	1
β-strand	815-826	12	1
β-strand	830-838	9	1
α-helix	840-845	6
α-helix	850-854	5
α-helix	858-860	3
α-helix	865-870	6
β-strand	872-878	7	1

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	12-15	4	7
β-strand	22	1	8
α-helix	23-34	12
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	61-62	2
β-strand	66-71	6	7
β-strand	75	1	3

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-34	12
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	61-62	2
β-strand	66-71	6	9

Chain D: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	584-585	2	11
β-strand	588-589	2	12
α-helix	596-606	11
α-helix	613-616	4
α-helix	628-633	6
α-helix	634-640	7
α-helix	641-646	6
β-strand	648-649	2	12
α-helix	651-664	14
β-strand	675	1	13
α-helix	677-682	6
α-helix	683-688	6
β-strand	695-699	5	14
β-strand	703-707	5	14
β-strand	710-711	2	11
β-strand	724	1	15
α-helix	725-735	11
β-strand	740	1	14
β-strand	746-750	5	11
β-strand	753	1	16
β-strand	759	1	16
β-strand	765	1	15
β-strand	769-771	3	11
α-helix	773-775	3
β-strand	776	1	14
β-strand	788-797	10	11
β-strand	802-807	6	11
β-strand	815-826	12	11
β-strand	830-838	9	11
α-helix	840-845	6
α-helix	850-854	5
α-helix	858-860	3
α-helix	865-870	6
β-strand	872-878	7	11

Chain E: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
β-strand	12-16	5	17
β-strand	22	1	18
α-helix	23-34	12
β-strand	41-45	5	17
β-strand	48-49	2	17
α-helix	50-51	2
β-strand	55	1	18
α-helix	61-62	2
β-strand	66-71	6	17
β-strand	75	1	13

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	19
β-strand	12-16	5	19
β-strand	22	1	20
α-helix	23-34	12
β-strand	41-45	5	19
β-strand	48-49	2	19
α-helix	50-51	2
β-strand	55	1	20
β-strand	66-71	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein	A, D	protein	312	Danio rerio	E7FEV5 (AlphaFold model)
Ubiquitin	B, E	protein	76	Mus musculus	P0CG50 (AlphaFold model)
Ubiquitin	C, F	protein	72	Mus musculus	P0CG50 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3WXG_1 Uncharacterized protein (chains A, D)
SHMGLEVMVGKKKGIQGHYNSAYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQEL
LRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEEKDPEEFLNILFHHILRVDPL
LRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRF
GKDFKMFNKIFPSLELDITDLLDDTPLEGGPHQQMELFAVLCIETSHYVAFVKYGSADSA
WLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYM
CMYQSPTMSLYK

Sequence of entity 2 (B, E), FASTA

>3WXG_2 Ubiquitin (chains B, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG

Sequence of entity 3 (C, F), FASTA

>3WXG_3 Ubiquitin (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLR

Primary citation

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity. Sato, Y., Goto, E., Shibata, Y. et al. Nat Struct Mol Biol (2015) 22:222-229. DOI 10.1038/nsmb.2970 · PubMed

Other PDB entries of the same protein (UniProt E7FEV5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WXF 2.3 Å, Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin
3WXE 2.5 Å, Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin

Browse structure collections

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