9D3O: 167-bp 5S rDNA nucleosome - closed

167-bp 5S rDNA nucleosome - closed. Determined by electron microscopy at 3.0 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Xenopus borealis
Chains: 10
Atoms: 12,037
Mol. weight: 176.61 kDa
Released: 13 Aug 2025

Explore 9D3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D3O contains 38 α-helices and 20 β-strands across 8 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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-74	11
α-helix	75-77	3
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	83-92	10
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	5
α-helix	47-71	25
β-strand	77-78	2	4
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	8

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
α-helix	40-48	9
β-strand	53-54	2	4
α-helix	56-83	28
β-strand	88-89	2	5
α-helix	91-101	11
α-helix	104-122	19

Chain 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	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-92	10
β-strand	96-98	3	8

Chain G: 6 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	47-72	26
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	9
α-helix	54-81	28
β-strand	86-87	2	10
α-helix	89-99	11
α-helix	102-120	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	99	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	82	Homo sapiens	P62805 (AlphaFold model)
Histone H2B type 1-M	D, H	protein	95	Homo sapiens	Q99879 (AlphaFold model)
DNA (noncoding strand)	I	DNA	145	Xenopus borealis
DNA (coding strand)	J	DNA	145	Xenopus borealis
Histone H2A type 2-A	C, G	protein	109	Homo sapiens	Q6FI13 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>9D3O_1 Histone H3.2 (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9D3O_2 Histone H4 (chains B, F)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (D, H), FASTA

>9D3O_3 Histone H2B type 1-M (chains D, H)
RKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

Sequence of entity 4 (I), FASTA

>9D3O_4 DNA (noncoding strand) (chains I)
CTTGTTTTCCTGCCTGGGGGAAAAGACCCTGGCATGGGGAGGAGCTGGGCCCCCCCCAGA
AGGCAGCACAAGGGGAGGAAAAGTCAGCCTTGTGCTCGCCTACGGCCATACCACCCTGAA
AGTGCCCGATATCGTCTGATCTCGG

Sequence of entity 5 (J), FASTA

>9D3O_5 DNA (coding strand) (chains J)
CCGAGATCAGACGATATCGGGCACTTTCAGGGTGGTATGGCCGTAGGCGAGCACAAGGCT
GACTTTTCCTCCCCTTGTGCTGCCTTCTGGGGGGGGCCCAGCTCCTCCCCATGCCAGGGT
CTTTTCCCCCAGGCAGGAAAACAAG

Sequence of entity 6 (C, G), FASTA

>9D3O_6 Histone H2A type 2-A (chains C, G)
RAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK

Primary citation

Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif. Alegrio-Louro, J., Cruz-Becerra, G., Kassavetis, G.A. et al. Genes Dev (2025) 39:1155-1161. DOI 10.1101/gad.352720.125 · PubMed

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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