8UQ9: PDB entry 8UQ9

Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker. Determined by X-ray diffraction at 2.3 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,314
Mol. weight: 100.03 kDa
Ligands: ZN
Released: 17 Jan 2024

Explore 8UQ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UQ9 contains 50 α-helices and 38 β-strands across 2 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: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-10	3
α-helix	12-14	3
β-strand	15	1	8
β-strand	22	1	8
α-helix	23	1
β-strand	27-28	2	9
β-strand	34-35	2	9
α-helix	37-40	4
α-helix	41-48	8
β-strand	50	1	10
β-strand	57	1	10
α-helix	59-67	9
β-strand	72	1	9
α-helix	74-83	10
α-helix	85-90	6
α-helix	1002-1015	14
α-helix	1017-1018	2
β-strand	1021-1025	5	11
β-strand	1032-1038	7	11
α-helix	1039-1040	2
β-strand	1049-1055	7	11
β-strand	1066-1069	4	11
β-strand	1075	1	12
β-strand	1078	1	12
β-strand	1083	1	11
β-strand	1084	1	12
α-helix	1087-1089	3
α-helix	1099-1111	13
α-helix	1121-1129	9
α-helix	1131-1145	15
α-helix	2038-2048	11
β-strand	2053-2054	2	13
α-helix	2056-2083	28
β-strand	2088-2089	2	14
α-helix	2091-2101	11
α-helix	2104-2122	19
α-helix	3017-3021	5
α-helix	3027-3036	10
β-strand	3042-3043	2	14
α-helix	3046-3072	27
β-strand	3077-3078	2	13
α-helix	3080-3089	10
α-helix	3091-3097	7

Chain A: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-10	3
α-helix	12-14	3
β-strand	15	1	1
β-strand	22	1	1
α-helix	23	1
β-strand	27-28	2	2
β-strand	34-35	2	2
α-helix	37-39	3
α-helix	40-48	9
β-strand	50	1	3
β-strand	57	1	3
α-helix	59-67	9
β-strand	72	1	2
α-helix	74-83	10
α-helix	85-90	6
α-helix	1002-1015	14
β-strand	1022-1025	4	4
β-strand	1032-1038	7	4
α-helix	1039-1040	2
β-strand	1049-1055	7	4
α-helix	1064-1065	2
β-strand	1066-1069	4	4
β-strand	1075	1	5
β-strand	1078	1	5
β-strand	1083	1	4
β-strand	1084	1	5
α-helix	1087-1089	3
α-helix	1099-1111	13
α-helix	1121-1129	9
α-helix	1131-1145	15
α-helix	2038-2048	11
β-strand	2053-2054	2	6
α-helix	2056-2083	28
β-strand	2088-2089	2	7
α-helix	2091-2101	11
α-helix	2104-2122	19
α-helix	3017-3021	5
α-helix	3027-3036	10
β-strand	3042-3043	2	7
α-helix	3046-3072	27
β-strand	3077-3078	2	6
α-helix	3080-3089	10
α-helix	3091-3097	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone…	A, a	protein	439	Homo sapiens	P04908 (AlphaFold model), P61077 (AlphaFold model), Q16778 (AlphaFold model), Q8IYW5 (AlphaFold model)

Sequence of entity 1 (A, a), FASTA

>8UQ9_1 E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E (chains A, a)
GHMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV
SSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGSGSGSGSALKRINKELSDLARDPP
AQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNI
NSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRIS
REWTQKYAMGSGGRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR
LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSAKAKTRSSRAGLQFP
VGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA
IRNDEELNKLLGRVTIAQG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Hu, Q., Zhao, D., Cui, G. et al. Mol Cell (2024) 84:839-853.e12. DOI 10.1016/j.molcel.2023.12.036 · PubMed

Other PDB entries of the same protein (UniProt P04908 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VZ4 1.89 Å, Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA…
6ACL 1.92 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95
8I17 1.98 Å, Structural basis for H2A-H2B recognitions by human Spt16
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
5Y0D 1.99 Å, Crystal Structure of the human nucleosome containing the H2B E76K mutant
6IPU 1.99 Å, Human nucleosome core particle containing 145 bp of DNA
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5Y0C 2.09 Å, Crystal Structure of the human nucleosome at 2.09 angstrom resolution
8Q3E 2.17 Å, High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
5X7X 2.18 Å, The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution
5AV6 2.2 Å, human nucleosome core particle
5AV8 2.2 Å, human nucleosome core particle

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