9YCW: USP16 ZnF-UBP domain

Crystal structure of USP16 ZnF-UBP domain. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 May 2026.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,875
Mol. weight: 43.87 kDa
Ligands: ZN
Released: 20 May 2026

Explore 9YCW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YCW contains 16 α-helices and 15 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: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	19-22	4
β-strand	54-57	4	1
β-strand	63-65	3	1
α-helix	73-79	7
β-strand	88-91	4	1
β-strand	97-99	3	1
β-strand	104-106	3	1
α-helix	107	1
α-helix	113-125	13

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	19-22	4
α-helix	26-27	2
α-helix	32-35	4
β-strand	54-57	4	2
β-strand	63-65	3	2
α-helix	73-79	7
β-strand	88-91	4	2
β-strand	97-99	3	2
β-strand	104-106	3	2
α-helix	113-126	14

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	19-22	4
β-strand	54-57	4	3
β-strand	63-65	3	3
α-helix	73-79	7
β-strand	88-91	4	3
β-strand	97-99	3	3
β-strand	104-106	3	3
α-helix	107	1
α-helix	113-124	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 16	A, B, C	protein	125	Homo sapiens	Q9Y5T5 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9YCW_1 Ubiquitin carboxyl-terminal hydrolase 16 (chains A, B, C)
GPPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLKCGH
QGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCDNEVQYCSSNQLGQVVDYVR
KQASI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	9

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

Primary citation

The ZnF-UBP domain regulates USP16 activity by dislodging ubiquitin from the active site. Alexandrovics, J.A., Agrata, R., Schenk, P. et al. To be published.

Other PDB entries of the same protein (UniProt Q9Y5T5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8WG5 3.05 Å, Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome
2I50 Solution Structure of Ubp-M Znf-UBP domain

Browse structure collections

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