7PFD: Histone H3.2
Nucleosome 1 of the 4x197 nucleosome array containing H1. Determined by electron microscopy at 4.4 Å resolution. Released 3 Aug 2022.
- Method
- Electron microscopy
- Resolution
- 4.4 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 11
- Atoms
- 13,675
- Mol. weight
- 242.1 kDa
- Released
- 3 Aug 2022
Explore 7PFD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7PFD contains 42 α-helices and 22 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 | 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 | |
Chain B: 5 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 | 48-75 | 28 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 82 | 1 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-97 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| 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 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77 | 1 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53 | 1 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
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 | 136 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 147 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 126 | Homo sapiens | O60814 (AlphaFold model) |
| DNA (172-mer) | J | DNA | 172 | synthetic construct | |
| DNA (172-mer) | I | DNA | 172 | synthetic construct | |
| Histone H1.4 | U | protein | 218 | Homo sapiens | P10412 |
Sequence of entity 1 (A, E), FASTA
>7PFD_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7PFD_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7PFD_3 Histone H2A type 1-B/E (chains C, G)
HHHHHHENLYFQSNAPWMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSER
VGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTI
AQGGVLPNIQAVLLPKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>7PFD_4 Histone H2B type 1-K (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (J), FASTA
>7PFD_5 DNA (172-MER) (chains J)
CTTAATACTTACATGACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAAT
CCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCT
GTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGTATGGCGGCC
Sequence of entity 6 (I), FASTA
>7PFD_6 DNA (172-MER) (chains I)
GGCCGCCATACTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTCATGTAAGTATTAAG
Sequence of entity 7 (U), FASTA
>7PFD_7 Histone H1.4 (chains U)
SETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLAA
LKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAK
KAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAKP
KKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKK
Primary citation
Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Dombrowski, M., Engeholm, M., Dienemann, C. et al. Nat Struct Mol Biol (2022) 29:493-501. DOI 10.1038/s41594-022-00768-w · 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
Browse structure collections
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