7OWC: CYLD CAP-Gly3

Structure of CYLD CAP-Gly3 (467-565) bound to Ub; orthorhobic space group. Determined by X-ray diffraction at 1.85 Å resolution. Released 20 Oct 2021.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,802
Mol. weight: 38.53 kDa
Released: 20 Oct 2021

Explore 7OWC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OWC contains 14 α-helices and 36 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	470	1	3
β-strand	474	1	1
β-strand	475-478	4	4
α-helix	483	1
β-strand	484-492	9	4
β-strand	493	1	5
β-strand	501-506	6	4
β-strand	514	1	4
β-strand	517-518	2	6
β-strand	521-522	2	6
β-strand	531-535	5	4
α-helix	536-538	3
β-strand	539-541	3	4
α-helix	543-546	4
α-helix	548-550	3
α-helix	554-562	9

Chain C: 3 helices, 7 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
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	470	1	5
β-strand	474	1	7
β-strand	475-478	4	9
β-strand	484-492	9	9
β-strand	493	1	3
β-strand	501-506	6	9
β-strand	514	1	9
β-strand	517-518	2	10
β-strand	521-522	2	10
β-strand	531-535	5	9
α-helix	536-538	3
β-strand	539-541	3	9
α-helix	554-557	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-60S ribosomal protein L40	A, C	protein	76	Homo sapiens	P62987 (AlphaFold model)
Deubiquitinating enzyme CYLD	B, D	protein	99	Homo sapiens	Q9NQC7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7OWC_1 Ubiquitin-60S ribosomal protein L40 (chains A, C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLAGG

Sequence of entity 2 (B, D), FASTA

>7OWC_2 Deubiquitinating enzyme CYLD (chains B, D)
SHGLEVGSLAEVKENPPFYGVIRWIGQPPGLNEVLAGLELEDECAGCTDGTFRGTRYFTC
ALKKALFVKLKSCRPDSRFASLQPVSNQIERCNSLAFGG

Primary citation

Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains. Elliott, P.R., Leske, D., Wagstaff, J. et al. Cell Rep (2021) 37:109777-109777. DOI 10.1016/j.celrep.2021.109777 · PubMed

Other PDB entries of the same protein (UniProt P62987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
4PIH 1.5 Å, X-ray crystal structure of the K33S mutant of ubiquitin
4PIJ 1.5 Å, X-ray crystal structure of the K11S/K63S double mutant of ubiquitin
5GOJ 1.55 Å, Lys63-linked di-ubiquitin
5J8P 1.55 Å, Lys27-linked diubiquitin
5GOI 1.59 Å, Lys48-linked di-ubiquitin
8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
5GOC 1.73 Å, Lys11-linked diubiquitin
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
4HJK 1.78 Å, U7Ub7 Disulfide variant

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