6X0N: Histone H3.2
Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin. Determined by electron microscopy at 10.0 Å resolution. Released 16 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 10.0 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 23
- Atoms
- 32,248
- Mol. weight
- 597.24 kDa
- Released
- 16 Sept 2020
Explore 6X0N in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6X0N contains 110 α-helices and 76 β-strands across 19 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, A, e and E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 11 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 12 |
| α-helix | 121-131 | 11 | |
Chains b, B and F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 12 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 11 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 13 |
Chain c: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 14 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 15 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 16 |
| α-helix | 113-115 | 3 | |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chains d and h: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 15 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 14 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-30 | 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 | 102-121 | 20 | |
Chain f: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 18 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 17 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 16 |
Chain g: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 19 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 20 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 13 |
| α-helix | 113-115 | 3 | |
5 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, a, e | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F, b, f | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G, c, g | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H, d, h | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (167-mer) | I, i | DNA | 167 | synthetic construct | |
| DNA (167-mer) | J, j | DNA | 167 | synthetic construct | |
| Histone PARylation factor 1 | O | protein | 356 | Homo sapiens | Q9NWY4 |
| Poly [ADP-ribose] polymerase 2 | P, R | protein | 590 | Homo sapiens | Q9UGN5 |
Sequence of entity 1 (A, E, a, e), FASTA
>6X0N_1 Histone H3.2 (chains A, E, a, e)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F, b, f), FASTA
>6X0N_2 Histone H4 (chains B, F, b, f)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G, c, g), FASTA
>6X0N_3 Histone H2A (chains C, G, c, g)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H, d, h), FASTA
>6X0N_4 Histone H2B 1.1 (chains D, H, d, h)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (I, i), FASTA
>6X0N_5 DNA (167-MER) (chains I, i)
CAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCATCATAG
Sequence of entity 6 (J, j), FASTA
>6X0N_6 DNA (167-MER) (chains J, j)
CTATGATGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTG
Sequence of entity 7 (O), FASTA
>6X0N_7 Histone PARylation factor 1 (chains O)
MGHHHHHHGGMVGGGGKRRPGGEGPQCEKTTDVKKSKFCEADVSSDLRKEVENHYKLSLP
EDFYHFWKFCEELDPEKPSDSLSASLGLQLVGPYDILAGKHKTKKKSTGLNFNLHWRFYY
DPPEFQTIIIGDNKTQYHMGYFRDSPDEFPVYVGINEAKKNCIIVPNGDNVFAAVKLFLT
KKLKEITDKKKINLLKNIDEKLTEAARELGYSLEQRTVKMKQRDKKVVTKTFHGAGLVVP
VDKNDVGYRELPETDADLKRICKTIVEAASDEERLKAFAPIQEMMTFVQFANDECDYGMG
LELGMDLFCYGSHYFHKVAGQLLPLAYNLLKRNLFAEIIEEHLANRSQENIDQLAA
Sequence of entity 8 (P, R), FASTA
>6X0N_8 Poly [ADP-ribose] polymerase 2 (chains P, R)
MGSSHHHHHHSSGLVPRGSHMAARRRRSTGGGRARALNESKRVNNGNTAPEDSSPAKKTR
RCQRQESKKMPVAGGKANKDRTEDKQDESVKALLLKGKAPVDPECTAKVGKAHVYCEGND
VYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSVWMRWGRVGKMGQHSLVACSGNLNKAK
EIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMDYATNTQDEEETKKEESLKSPLKPESQ
LDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQ
HGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQS
PEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEK
EAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANY
CFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNG
STVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW
Primary citation
Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin. Bilokapic, S., Suskiewicz, M.J., Ahel, I. et al. Nature (2020) 585:609-613. DOI 10.1038/s41586-020-2725-7 · 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
Browse structure collections
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