9KQO: RNF20/RNF40-RAD6A-Ub

cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome. Determined by electron microscopy at 3.48 Å resolution. Released 31 Dec 2025.

Method: Electron microscopy
Resolution: 3.48 Å
Organism: Homo sapiens
Chains: 14
Atoms: 14,687
Mol. weight: 239.8 kDa
Ligands: NAG, ZN
Released: 31 Dec 2025

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

Secondary structure: helices and β-sheets

9KQO contains 49 α-helices and 46 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	942-946	5
β-strand	947	1	1
β-strand	955	1	1
β-strand	958-960	3	2
β-strand	966-967	2	2
α-helix	970-977	8
β-strand	995-997	3	2

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	3
β-strand	48-49	2	3
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-70	5	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	5
α-helix	46-72	27
β-strand	77-78	2	6
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	7

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	6
α-helix	56-83	28
β-strand	88-89	2	5
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	64-78	15
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	118-119	2	9
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	9
α-helix	50-75	26
β-strand	80-81	2	8
α-helix	83-91	9
β-strand	96-98	3	7

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	10
α-helix	46-73	28
β-strand	77-78	2	11
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	12

Chain H: 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

4 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
E3 ubiquitin-protein ligase BRE1B	A	protein	60	Homo sapiens	O75150 (AlphaFold model)
Polyubiquitin-B	B	protein	75	Homo sapiens	J3QS39 (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)
Histone H3	E, K	protein	135	Homo sapiens	A0A653DHJ5
Histone H4	F, L	protein	102	Homo sapiens	P62805
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens
E3 ubiquitin-protein ligase BRE1A	M	protein	60	Homo sapiens	Q5VTR2
Ubiquitin-conjugating enzyme E2 A	R	protein	150	Homo sapiens	P49459

Sequence of entity 1 (A), FASTA

>9KQO_1 E3 ubiquitin-protein ligase BRE1B (chains A)
EYKARLTCPCCNTRKKDAVLTKCFHVFCFECVRGRYEARQRKCPKCNAAFGAHDFHRIYI

Sequence of entity 2 (B), FASTA

>9KQO_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Sequence of entity 3 (C, G), FASTA

>9KQO_3 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>9KQO_4 Histone H2B type 1-K (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTC
YTSAK

Sequence of entity 5 (E, K), FASTA

>9KQO_5 Histone H3 (chains E, K)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 6 (F, L), FASTA

>9KQO_6 Histone H4 (chains F, L)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 7 (I), FASTA

>9KQO_7 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 8 (J), FASTA

>9KQO_8 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Sequence of entity 9 (M), FASTA

>9KQO_9 E3 ubiquitin-protein ligase BRE1A (chains M)
DYKARLTCPCCNMRKKDAVLTKCFHVFCFECVKTRYDTRQRKCPKCNAAFGANDFHRIYI

Sequence of entity 10 (R), FASTA

>9KQO_10 Ubiquitin-conjugating enzyme E2 A (chains R)
MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFT
EEYPNKPPTVRFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNS
PANSQAAQLYQENKREYEKRVSAIVEQSWR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
ZN	Zinc ion	Zn	4

Primary citation

Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation. Deng, Z., Tao, S., Du, Y. et al. Nat Chem Biol (2026) 22:740-750. DOI 10.1038/s41589-025-02109-6 · PubMed

Other PDB entries of the same protein (UniProt O75150 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GUJ 2.8 Å, Bre1-nucleosome complex (Model II)
8GUI 2.81 Å, Bre1-nucleosome complex (Model I)
8IEJ 3.12 Å, RNF20-RNF40/hRad6A-Ub/nucleosome complex

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