8WG5: USP16

Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome. Determined by electron microscopy at 3.05 Å resolution. Released 27 Dec 2023.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,965
Mol. weight: 279.47 kDa
Released: 27 Dec 2023

Explore 8WG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WG5 contains 51 α-helices and 46 β-strands across 10 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	9

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-36	9
β-strand	42-43	2	10
α-helix	46-72	27
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	12
α-helix	117-118	2

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	11
α-helix	56-83	28
β-strand	88-89	2	10
α-helix	91-101	11
α-helix	104-123	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-74	11
β-strand	83-84	2	13
α-helix	86-113	28
β-strand	118-119	2	14
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	14
α-helix	51-75	25
β-strand	80-81	2	13
α-helix	83-91	9
β-strand	96-98	3	12

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	28-36	9
β-strand	42-43	2	15
α-helix	46-72	27
β-strand	77-78	2	16
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	9

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	38-48	11
β-strand	53-54	2	16
α-helix	56-83	28
β-strand	88-89	2	15
α-helix	91-101	11
α-helix	104-123	20

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 16	M	protein	823	Homo sapiens	Q9Y5T5 (AlphaFold model)
Histone H3.1	A, E	protein	98	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	79	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	111	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	94	Homo sapiens	O60814
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens
Ubiquitin B	U	protein	76	Homo sapiens	P0CG47

Sequence of entity 1 (M), FASTA

>8WG5_1 Ubiquitin carboxyl-terminal hydrolase 16 (chains M)
MGKKRTKGKTVPIDDSSETLEPVCRHIRKGLEQGNLKKALVNVEWNICQDCKTDNKVKDK
AEEETEEKPSVWLCLKCGHQGCGRNSQEQHALKHYLTPRSEPHCLVLSLDNWSVWCYVCD
NEVQYCSSNQLGQVVDYVRKQASITTPKPAEKDNGNIELENKKLEKESKNEQEREKKENM
AKENPPMNSPCQITVKGLSNLGNTCFFNAVMQNLSQTPVLRELLKEVKMSGTIVKIEPPD
LALTEPLEINLEPPGPLTLAMSQFLNEMQETKKGVVTPKELFSQVCKKAVRFKGYQQQDS
QELLRYLLDGMRAEEHQRVSKGILKAFGNSTEKLDEELKNKVKDYEKKKSMPSFVDRIFG
GELTSMIMCDQCRTVSLVHESFLDLSLPVLDDQSGKKSVNDKNLKKTVEDEDQDSEEEKD
NDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSE
YEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNI
NMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHT
PGTKVYEVVNEDPETAFCTLANREVFNTDECSIQHCLYQFTRNEKLRDANKLLCEVCTRR
QCNGPKANIKGERKHVYTNAKKQMLISLAPPVLTLHLKRFQQAGFNLRKVNKHIKFPEIL
DLAPFCTLKCKNVAEENTRVLYSLYGVVEHSGTMRSGHYTAYAKARTANSHLSNLVLHGD
IPQDFEMESKGQWFHISDTHVQAVPTTKVLNSQAYLLFYERIL

Sequence of entity 2 (A, E), FASTA

>8WG5_2 Histone H3.1 (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAC
EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

Sequence of entity 3 (B, F), FASTA

>8WG5_3 Histone H4 (chains B, F)
RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVT
AMDVVYALKRQGRTLYGFG

Sequence of entity 4 (C, G), FASTA

>8WG5_4 Histone H2A type 1-B/E (chains C, G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKCT

Sequence of entity 5 (D, H), FASTA

>8WG5_5 Histone H2B type 1-K (chains D, H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Sequence of entity 6 (I), FASTA

>8WG5_6 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 7 (J), FASTA

>8WG5_7 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Sequence of entity 8 (U), FASTA

>8WG5_8 Ubiquitin B (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Primary citation

Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Ai, H., He, Z., Deng, Z. et al. Nat Struct Mol Biol (2024) 31:1745-1755. DOI 10.1038/s41594-024-01342-2 · PubMed

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

9YCW 1.8 Å, Crystal structure of USP16 ZnF-UBP domain
2I50 Solution Structure of Ubp-M Znf-UBP domain

Browse structure collections

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