6NN6: Dot1L-H2BK120ub nucleosome complex
Structure of Dot1L-H2BK120ub nucleosome complex. Determined by electron microscopy at 3.9 Å resolution. Released 13 Feb 2019.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 12
- Atoms
- 15,125
- Mol. weight
- 254.26 kDa
- Released
- 13 Feb 2019
Explore 6NN6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6NN6 contains 58 α-helices and 34 β-strands across 10 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: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 85 | 1 | |
| α-helix | 88-113 | 26 | |
| β-strand | 119 | 1 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-48 | 9 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 58-83 | 26 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 47-54 | 8 | |
| α-helix | 65-74 | 10 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 87-113 | 27 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 124-130 | 7 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-41 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 53-75 | 23 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-33 | 7 | |
| α-helix | 47-70 | 24 | |
| α-helix | 80-88 | 9 | |
| α-helix | 92-96 | 5 | |
| β-strand | 100-102 | 3 | 3 |
Chain H: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-46 | 9 | |
| α-helix | 59-73 | 15 | |
| α-helix | 77-82 | 6 | |
| α-helix | 93-101 | 9 | |
| α-helix | 104-123 | 20 | |
2 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 | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A type 1 | C, G | protein | 129 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 124 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (145-mer) | I | DNA | 145 | synthetic construct | |
| DNA (145-mer) | J | DNA | 145 | synthetic construct | |
| Histone-lysine N-methyltransferase, H3 lysine-79 specific | K | protein | 416 | Homo sapiens | Q8TEK3 |
| Ubiquitin | L | protein | 80 | Homo sapiens | F5H388 |
Sequence of entity 1 (A, E), FASTA
>6NN6_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6NN6_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6NN6_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6NN6_4 Histone H2B 1.1 (chains D, H)
GSAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSI
MNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCY
TSAK
Sequence of entity 5 (I), FASTA
>6NN6_5 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>6NN6_6 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 7 (K), FASTA
>6NN6_7 Histone-lysine N-methyltransferase, H3 lysine-79 specific (chains K)
GSEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVL
IDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVT
DPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCK
HHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFV
NNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLK
GSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGP
EGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLNKKGRKMAGRKRGRPKK
Sequence of entity 8 (L), FASTA
>6NN6_8 Ubiquitin (chains L)
GSGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGC
Primary citation
Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase. Anderson, C.J., Baird, M.R., Hsu, A. et al. Cell Rep (2019) 26:1681-1690.e5. DOI 10.1016/j.celrep.2019.01.058 · 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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