6NOG: Poised-state Dot1L
Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome. Determined by electron microscopy at 3.9 Å resolution. Released 20 Feb 2019.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Xenopus laevis, Homo sapiens, synthetic construct
- Chains
- 12
- Atoms
- 14,929
- Mol. weight
- 254.69 kDa
- Released
- 20 Feb 2019
Explore 6NOG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6NOG contains 57 α-helices and 36 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| α-helix | 50-75 | 26 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-97 | 2 | 4 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101 | 1 | 5 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
| β-strand | 53-54 | 2 | 7 |
| α-helix | 56-82 | 27 | |
| β-strand | 88-89 | 2 | 6 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-121 | 17 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 84 | 1 | 2 |
| α-helix | 86-112 | 27 | |
| β-strand | 118 | 1 | 3 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45 | 1 | 3 |
| α-helix | 51-74 | 24 | |
| β-strand | 81 | 1 | 2 |
| α-helix | 83-93 | 11 | |
| β-strand | 97 | 1 | 5 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 4 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 56-82 | 27 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 93-101 | 9 | |
| α-helix | 104-121 | 18 | |
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 | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| Ubiquitin | L | protein | 80 | Homo sapiens | J3QS39 |
| Histone-lysine N-methyltransferase, H3 lysine-79 specific | K | protein | 416 | Homo sapiens | Q8TEK3 |
| 601 DNA Strand 1 | I | DNA | 146 | synthetic construct | |
| 601 DNA Strand 2 | J | DNA | 146 | synthetic construct | |
Sequence of entity 1 (A, E), FASTA
>6NOG_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6NOG_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6NOG_3 Histone H2A type 1 (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6NOG_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTS
AK
Sequence of entity 5 (L), FASTA
>6NOG_5 Ubiquitin (chains L)
GSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGC
Sequence of entity 6 (K), FASTA
>6NOG_6 Histone-lysine N-methyltransferase, H3 lysine-79 specific (chains K)
GGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVL
IDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVT
DPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCK
HHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFV
NNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLK
GSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGP
EGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLNKKGRKMAGRKRGRPKK
Sequence of entity 7 (I), FASTA
>6NOG_7 601 DNA Strand 1 (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT
Sequence of entity 8 (J), FASTA
>6NOG_8 601 DNA Strand 2 (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA
Primary citation
Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Worden, E.J., Hoffmann, N.A., Hicks, C.W. et al. Cell (2019) 176:1490-1501.e12. DOI 10.1016/j.cell.2019.02.002 · 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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