9KQ2: RNF168'-RNF168-UbcH5c complex

Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome. Determined by electron microscopy at 3.9 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 11
Atoms: 12,514
Mol. weight: 210.82 kDa
Ligands: ZN
Released: 12 Nov 2025

Explore 9KQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KQ2 contains 41 α-helices and 26 β-strands across 9 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118	1	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45	1	2
α-helix	50-76	27
β-strand	80-81	2	1
α-helix	83-92	10
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	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-120	20

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45	1	8
α-helix	50-76	27
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
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 K: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	11
β-strand	22	1	11
β-strand	27-28	2	12
β-strand	34-35	2	12
α-helix	37-40	4
α-helix	41-45	5
β-strand	50	1	13
β-strand	57	1	13
α-helix	59-68	10
α-helix	74-83	10
α-helix	85-92	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	135	Xenopus laevis	A0A310TTQ1 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	A0A8J1LTD2 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B	D, H	protein	122	Xenopus laevis	A0A8J0U496 (AlphaFold model)
DNA (147-mer)	I	DNA	147	Homo sapiens
DNA (147-mer)	J	DNA	147	Homo sapiens
E3 ubiquitin-protein ligase RNF168	K	protein	103	Homo sapiens	Q8IYW5

Sequence of entity 1 (A, E), FASTA

>9KQ2_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9KQ2_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9KQ2_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9KQ2_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>9KQ2_5 DNA (147-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>9KQ2_6 DNA (147-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 7 (K), FASTA

>9KQ2_7 E3 ubiquitin-protein ligase RNF168 (chains K)
MALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS
WTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

AlphaFold-guided structural analyses of nucleosome binding proteins. Yang, X., Zhu, H., Shi, L. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf735 · PubMed

Other PDB entries of the same protein (UniProt A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome

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