3WXF: CYLD USP domain

Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Feb 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Danio rerio, Homo sapiens
Chains: 4
Atoms: 7,358
Mol. weight: 105.68 kDa
Released: 11 Feb 2015

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

Secondary structure: helices and β-sheets

3WXF contains 52 α-helices and 68 β-strands across 4 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	579-581	3
β-strand	584-585	2	1
β-strand	588-589	2	2
α-helix	590-591	2
α-helix	596-606	11
α-helix	613-616	4
α-helix	618-620	3
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	677-681	5
α-helix	682-688	7
α-helix	691-693	3
β-strand	695-699	5	4
β-strand	705-707	3	4
β-strand	710-711	2	1
β-strand	724	1	5
α-helix	725-735	11
β-strand	738-740	3	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	815-825	11	1
β-strand	831-838	8	1
α-helix	841-845	5
α-helix	850-854	5
α-helix	858-860	3
α-helix	865-870	6
β-strand	872-878	7	1

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7
β-strand	75	1	3
β-strand	79-82	4	9
β-strand	88-91	4	9
β-strand	98	1	10
α-helix	99-109	11
α-helix	114-116	3
β-strand	117-121	5	9
β-strand	124-125	2	9
α-helix	126-127	2
β-strand	131	1	10
β-strand	142-147	6	9

Chain C: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	579-581	3
β-strand	584-585	2	11
β-strand	588-589	2	12
α-helix	590-591	2
α-helix	596-606	11
α-helix	613-616	4
α-helix	618-620	3
α-helix	625	1
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
α-helix	677-681	5
α-helix	682-688	7
α-helix	691-693	3
β-strand	695-699	5	13
β-strand	704-707	4	13
β-strand	710-711	2	11
β-strand	724	1	14
α-helix	725-735	11
β-strand	738-740	3	13
β-strand	746-750	5	11
β-strand	753	1	15
β-strand	759	1	15
β-strand	765	1	14
β-strand	769-771	3	11
α-helix	773-775	3
β-strand	776	1	13
β-strand	788-797	10	11
β-strand	802-807	6	11
β-strand	815-825	11	11
β-strand	831-838	8	11
α-helix	841-845	5
α-helix	850-854	5
α-helix	858-860	3
α-helix	865-870	6
β-strand	872-878	7	11

Chain D: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-49	2	16
α-helix	50-51	2
β-strand	55	1	17
α-helix	57-59	3
β-strand	66-71	6	16
α-helix	72-73	2
β-strand	77-82	6	18
β-strand	88-93	6	18
β-strand	98	1	19
α-helix	99-110	12
α-helix	114-116	3
β-strand	117-121	5	18
β-strand	124-125	2	18
α-helix	126-127	2
β-strand	131	1	19
β-strand	142-147	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein	A, C	protein	312	Danio rerio	E7FEV5 (AlphaFold model)
Ubiquitin	B, D	protein	148	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3WXF_1 Uncharacterized protein (chains A, C)
SHMGLEVMVGKKKGIQGHYNSSYLDSTLFCLFSFSSVLDTVLLRPRSKTDVEYYKETQEL
LRTEIVNPLRIHGYVCATKIMKLRRILEKVEAASGFTSEQKDPEEFLNILFHHILRVDPL
LRLRSAGQKVQDCYFYQIFMDKKDKVMVPTSQQLLEWSFINSDLKFAEAPSCLIIQMPRF
GKDFKMFNKIFPSLELDITDLLDDTPLEGGPHQQMELFAVLCIETSHYVAFVKYGSADSA
WLFFDSMADRDGGQNGFNIPQVSRCPEVGEYLKMTPEELHALDPKNIQGYARRLLCDAYM
CMYQSPTMSLYK

Sequence of entity 2 (B, D), FASTA

>3WXF_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLR

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:

3WXE 2.5 Å, Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
3WXG 3.1 Å, Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin

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