7XCT: Ubiquitin
Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex. Determined by electron microscopy at 2.72 Å resolution. Released 20 Apr 2022.
- Method
- Electron microscopy
- Resolution
- 2.72 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 14
- Atoms
- 18,633
- Mol. weight
- 271.32 kDa
- Ligands
- SAM
- Released
- 20 Apr 2022
Explore 7XCT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7XCT contains 83 α-helices and 59 β-strands across 12 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: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-77 | 3 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 14 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 14 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 10 |
Chains C and G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 16 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 15 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| α-helix | 97-99 | 3 | |
| β-strand | 100-102 | 3 | 7 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 15 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 16 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain E: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| α-helix | 75-78 | 4 | |
| α-helix | 86-112 | 27 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 121-131 | 11 | |
Chain F: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-34 | 4 | |
| α-helix | 37-40 | 4 | |
| β-strand | 45-46 | 2 | 4 |
| α-helix | 50-53 | 4 | |
| β-strand | 69 | 1 | 5 |
| β-strand | 71 | 1 | 5 |
| β-strand | 84 | 1 | 6 |
| β-strand | 87 | 1 | 6 |
| β-strand | 90 | 1 | 6 |
| β-strand | 96-98 | 3 | 7 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
Chains K and M: 19 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 11 |
| β-strand | 19-20 | 2 | 11 |
| α-helix | 37-44 | 8 | |
| α-helix | 51-54 | 4 | |
| α-helix | 69-72 | 4 | |
| α-helix | 76-79 | 4 | |
| α-helix | 83-86 | 4 | |
| α-helix | 87-89 | 3 | |
| α-helix | 101-103 | 3 | |
| α-helix | 106-118 | 13 | |
| α-helix | 122-126 | 5 | |
| β-strand | 139 | 1 | 12 |
| α-helix | 141-151 | 11 | |
| β-strand | 159-162 | 4 | 13 |
| α-helix | 168-174 | 7 | |
| β-strand | 181-186 | 6 | 13 |
| α-helix | 189-208 | 20 | |
| β-strand | 215-220 | 6 | 13 |
| α-helix | 226-233 | 8 | |
| β-strand | 237-240 | 4 | 13 |
| α-helix | 247-254 | 8 | |
| α-helix | 257-259 | 3 | |
| β-strand | 265-268 | 4 | 13 |
| α-helix | 287-289 | 3 | |
| β-strand | 291-295 | 5 | 13 |
| α-helix | 296-298 | 3 | |
| β-strand | 303 | 1 | 12 |
| α-helix | 309-311 | 3 | |
| β-strand | 313-317 | 5 | 13 |
| α-helix | 321-324 | 4 | |
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 |
|---|
| Ubiquitin | L, N | protein | 76 | Homo sapiens | P0CG47 (AlphaFold model) |
| Histone H4 | B, F | protein | 89 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A | C, G | protein | 108 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 93 | Homo sapiens | O60814 (AlphaFold model) |
| Histone-lysine N-methyltransferase, H3 lysine-79 specific | K, M | protein | 328 | Homo sapiens | Q8TEK3 |
| Histone domain-containing protein | A, E | protein | 99 | Homo sapiens | Q71DI3 |
| DNA (145-mer) | I | DNA | 145 | synthetic construct | |
| DNA (145-mer) | J | DNA | 145 | synthetic construct | |
Sequence of entity 1 (L, N), FASTA
>7XCT_1 Ubiquitin (chains L, N)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 2 (B, F), FASTA
>7XCT_2 Histone H4 (chains B, F)
MAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYT
EHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7XCT_3 Histone H2A (chains C, G)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 4 (D, H), FASTA
>7XCT_4 Histone H2B type 1-K (chains D, H)
SRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 5 (K, M), FASTA
>7XCT_5 Histone-lysine N-methyltransferase, H3 lysine-79 specific (chains K, M)
LELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYD
TKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEK
LNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYG
VEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFA
FGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVS
WTGKPVSYYLHTIDRTILENYFSSLKNP
Sequence of entity 6 (A, E), FASTA
>7XCT_6 Histone domain-containing protein (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFLTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 7 (I), FASTA
>7XCT_7 DNA (145-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGA
Sequence of entity 8 (J), FASTA
>7XCT_8 DNA (145-MER) (chains J)
TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTCGA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAM | S-adenosylmethionine | C15 H22 N6 O5 S | 2 |
Primary citation
H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity. Ai, H., Sun, M., Liu, A. et al. Nat Chem Biol (2022) 18:972-980. DOI 10.1038/s41589-022-01067-7 · PubMed
Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
- 5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
- 5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
- 4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
- 5GOD 1.15 Å, Lys27-linked di-ubiquitin
- 5GOB 1.15 Å, Lys6-linked di-ubiquitin
- 5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
- 7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
- 8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
- 5DK8 1.32 Å, Human ubiquitin in the P1 space group
- 7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
- 5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
Browse structure collections
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