8JLB: Histone H3.2

Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant. Determined by electron microscopy at 2.36 Å resolution. Released 4 Oct 2023.

Method
Electron microscopy
Resolution
2.36 Å
Organisms
Homo sapiens, synthetic construct
Chains
10
Atoms
11,844
Mol. weight
200.71 kDa
Released
4 Oct 2023

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

Secondary structure: helices and β-sheets

8JLB contains 40 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.

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

ElementResiduesLengthSheet
α-helix41-422
α-helix45-5612
α-helix64-7613
β-strand83-8421
α-helix86-11328
β-strand118-11922
α-helix121-13111
Chains B and F: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix31-4010
β-strand45-4622
α-helix50-7526
β-strand80-8121
α-helix83-9210
β-strand96-9833
Chains C and G: 7 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix12-143
α-helix17-215
α-helix27-359
β-strand42-4324
α-helix46-7227
β-strand77-7825
α-helix80-889
α-helix91-966
β-strand100-10236
α-helix113-1153
Chains D and H: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix38-4811
β-strand53-5425
α-helix56-8328
β-strand88-8924
α-helix91-10111
α-helix105-12218

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Histone H3.2A, Eprotein135Homo sapiensQ71DI3 (AlphaFold model)
Histone H4B, Fprotein106Homo sapiensP62805 (AlphaFold model)
Histone H2A type 1-B/EC, Gprotein133Homo sapiensP04908 (AlphaFold model)
Histone H2B type 1-JD, Hprotein129Homo sapiensP06899 (AlphaFold model)
DNA (145-mer)IDNA145synthetic construct
DNA (145-mer)JDNA145synthetic construct
Sequence of entity 1 (A, E), FASTA
>8JLB_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8JLB_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8JLB_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>8JLB_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK
Sequence of entity 5 (I), FASTA
>8JLB_5 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>8JLB_6 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT

Primary citation

Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Oishi, T., Hatazawa, S., Kujirai, T. et al. Nucleic Acids Res (2023) 51:10364-10374. DOI 10.1093/nar/gkad754 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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