9F0O: Histone H3.2

The molecular basis and modulation of lamin-specific chromatin interaction. Determined by electron microscopy at 2.3 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 12
Atoms: 12,323
Mol. weight: 180.5 kDa
Released: 13 Aug 2025

Explore 9F0O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F0O contains 45 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chains B and F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
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	97-98	2	3

Chain C: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
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	101-102	2	6
α-helix	113-115	3
α-helix	117-118	2

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
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	101-121	21

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain G: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	17-21	5
α-helix	27-36	10
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
α-helix	100	1
β-strand	101-102	2	3
α-helix	113-115	3
α-helix	117-118	2

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-121	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	98	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	83	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	110	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	97	Xenopus laevis	P02281 (AlphaFold model)
601 wisdom DNA	I	DNA	147	Homo sapiens
601 wisdom DNA	J	DNA	147	Homo sapiens
laminA_peptide	K, L	protein	8	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>9F0O_1 Histone H3.2 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9F0O_2 Histone H4 (chains B, F)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9F0O_3 Histone H2A type 1 (chains C, G)
TRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK

Sequence of entity 4 (D, H), FASTA

>9F0O_4 Histone H2B 1.1 (chains D, H)
RRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 5 (I), FASTA

>9F0O_5 601 wisdom DNA (chains I)
TATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTA
AACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCC
AGGCACGTGTCAGATATATACATCCGA

Sequence of entity 6 (J), FASTA

>9F0O_6 601 wisdom DNA (chains J)
TCCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCGATA

Sequence of entity 7 (K, L), FASTA

>9F0O_7 laminA_peptide (chains K, L)
AEYNLRSR

Primary citation

The molecular basis of lamin-specific chromatin interactions. Wang, B., Kronenberg-Tenga, R., Rosti, V. et al. Nat Struct Mol Biol (2025) 32:1999-2011. DOI 10.1038/s41594-025-01622-5 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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