9U5U: The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub

The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome. Determined by electron microscopy at 3.12 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 14
Atoms: 16,392
Mol. weight: 313.34 kDa
Released: 14 Jan 2026

Explore 9U5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U5U contains 65 α-helices and 42 β-strands across 12 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	45-54	10
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
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	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	97-98	2	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-123	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	8
α-helix	51-75	25
β-strand	80-81	2	7
α-helix	83-91	9
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	3

Chain L: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	11
α-helix	12-22	11
β-strand	28-31	4	12
β-strand	46-52	7	12
α-helix	55-59	5
α-helix	75-79	5
α-helix	91-101	11
α-helix	110-118	9
α-helix	124-127	4
α-helix	130-132	3
α-helix	135-143	9
α-helix	148-150	3
β-strand	167-175	9	12
β-strand	180-184	5	12
β-strand	191-192	2	12
α-helix	203-217	15
β-strand	231-234	4	12
α-helix	237-240	4
α-helix	649-667	19
α-helix	672-685	14
α-helix	688-694	7
α-helix	699	1

3 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
Histone H3.2	A, E	protein	135	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	129	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	125	Homo sapiens	O60814 (AlphaFold model)
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens
Ubiquitin carboxyl-terminal hydrolase BAP1	L	protein	711	Homo sapiens	Q92560
Ubiquitin	M, O	protein	76	Homo sapiens	P62979
Polycomb group protein ASXL1	N	protein	159	Homo sapiens	Q8IXJ9

Sequence of entity 1 (A, E), FASTA

>9U5U_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9U5U_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9U5U_3 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>9U5U_4 Histone H2B type 1-K (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 5 (I), FASTA

>9U5U_5 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 6 (J), FASTA

>9U5U_6 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Sequence of entity 7 (L), FASTA

>9U5U_7 Ubiquitin carboxyl-terminal hydrolase BAP1 (chains L)
WLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFIFLFKWIEERRSRRKVST
LVDDTSVIDDDIVNNMFFAHQLIPNSCATHALLSVLLNCSSVDLGPTLSRMKDFTKGFSP
ESKGYAIGNAPELAKAHNSHARPEPRHLPEKQNGLSAVRTMEAFHFVSYVPITGRLFELD
GLKVYPIDHGPWGEDEEWTDKARRVIMERIGLATAGEPYHDIRFNLMAVVPDRRIKYEAR
LHVLKVNRQTVLEALQQLIRVTQPELIQTHKSQESQLPEESKSASNKSPLVLEANRAPAA
SEGNHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVHPNPTPIVQRLPAFLDNH
NYAKSPMQEEEDLAAGVGRSRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALRYKGKGTG
KPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSIPLSIKTSSGAGSPAVAVPTHSQP
SPTPSNESTDTASEIGSAFNSPLRSPIRSANPTRPSSPVTSHISKVLFGEDDSLLRVDCI
RYNRAVRDLGPVISTGLLHLAEDGVLSPLALTEGGKGSSPSIRPIQGSQGSSSPVEKEVV
EATDSREKTGMVRPGEPLSGEKYSPKELLALLKCVEAEIANYEACLKEEVEKRKKFKIDD
QRRTHNYDEFICTFISMLAQEGMLANLVEQNISVRRRQGVSIGRLHKQRKP

Sequence of entity 8 (M, O), FASTA

>9U5U_8 Ubiquitin (chains M, O)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 9 (N), FASTA

>9U5U_9 Polycomb group protein ASXL1 (chains N)
ATGQMKRNRGEEIDFETPGSILVNTNLRALINSRTFHALPSHFQQQLLFLLPEVDRQVGT
DGLLRLSSSALNNEFFTHAAQSWRERLADGEFTHEMQVRIRQEMEKEKKVEQWKEKFFED
YYGQKLGLTKEESLQQNVGQEEAEIKSGLCVPGHHHHHH

Primary citation

Unique Gluing Effect of ASXL1 K351 Monoubiquitination Stimulates PR-DUB-Mediated Nucleosomal H2AK119Ub Deubiquitination. Zhang, T., Zheng, J., Tong, Z. et al. bioRxiv (2025). DOI 10.1101/2025.04.25.650627

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

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