8ZJR: Nucleosome-bound RFX5 complex

Structure of nucleosome-bound RFX5 complex. Determined by electron microscopy at 3.3 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 12,213
Mol. weight: 219.82 kDa
Released: 13 Aug 2025

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

Secondary structure: helices and β-sheets

8ZJR contains 40 α-helices and 23 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.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	46-57	12
α-helix	65-76	12
β-strand	84-85	2	1
α-helix	89-114	26
β-strand	119-120	2	2
α-helix	122-132	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-42	11
β-strand	46-47	2	2
α-helix	51-76	26
β-strand	81-82	2	1
α-helix	84-93	10
β-strand	98-99	2	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-37	10
β-strand	43-44	2	4
α-helix	48-73	26
β-strand	78-79	2	5
α-helix	81-89	9
α-helix	92-97	6
β-strand	102-103	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	5
α-helix	57-84	28
β-strand	89-90	2	4
α-helix	92-102	11
α-helix	106-123	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	46-56	11
α-helix	65-76	12
β-strand	84-85	2	7
α-helix	87-114	28
β-strand	119-120	2	8
α-helix	122-131	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-42	11
β-strand	46-47	2	8
α-helix	52-76	25
β-strand	81-82	2	7
α-helix	84-93	10
β-strand	98-99	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	28-36	9
β-strand	43-44	2	9
α-helix	47-73	27
β-strand	78-79	2	10
α-helix	81-90	10
α-helix	92-97	6
β-strand	102-103	2	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	39-49	11
β-strand	54-55	2	10
α-helix	57-84	28
β-strand	89-90	2	9
α-helix	92-102	11
α-helix	106-124	19

1 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	138	Homo sapiens	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	107	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	132	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-K	D, H	protein	130	Homo sapiens	O60814 (AlphaFold model)
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct
DNA-binding protein RFX5	M	protein	148	Homo sapiens	P48382

Sequence of entity 1 (A, E), FASTA

>8ZJR_1 Histone H3.2 (chains A, E)
GPMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKS
TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRV
TIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8ZJR_2 Histone H4 (chains B, F)
MADLMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETR
GVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8ZJR_3 Histone H2A type 1-B/E (chains C, G)
GPMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEY
LTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP
KKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>8ZJR_4 Histone H2B type 1-K (chains D, H)
MADLMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGIS
SKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGT
KAVTKYTSAK

Sequence of entity 5 (I), FASTA

>8ZJR_5 DNA (147-MER) (chains I)
ATCCACACGTTACACGACGCTCTTCCGATCTTGGTTAGGGTGCAAGCATGATCCCTTCGA
TGAATAGAGCCGACTGGGCATAGTAACGCGTGGGTTGGTGAGGTGGTTCACGGTCATGCC
GCTTGGGTAAGCAGATCGGAAGAGGAT

Sequence of entity 6 (J), FASTA

>8ZJR_6 DNA (147-MER) (chains J)
ATCCTCTTCCGATCTGCTTACCCAAGCGGCATGACCGTGAACCACCTCACCAACCCACGC
GTTACTATGCCCAGTCGGCTCTATTCATCGAAGGGATCATGCTTGCACCCTAACCAAGAT
CGGAAGAGCGTCGTGTAACGTGTGGAT

Sequence of entity 7 (M), FASTA

>8ZJR_7 DNA-binding protein RFX5 (chains M)
MGSSHHHHHENLYFQGSDNDKLYLYLQLPSGPTTGDKSSEPSTLSNEEYMYAYRWIRNHL
EEHTDTCLPKQSVYDAYRKYCESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYC
YSGIRRKTLVSMPPLPGLDLKGSESPEM

Primary citation

Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5. Xue, W., Han, Y., Tian, Y. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf734 · 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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