8IEJ: RNF20-RNF40/hRad6A-Ub/nucleosome complex
RNF20-RNF40/hRad6A-Ub/nucleosome complex. Determined by electron microscopy at 3.12 Å resolution. Released 6 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.12 Å
- Organism
- Homo sapiens
- Chains
- 13
- Atoms
- 14,086
- Mol. weight
- 208.57 kDa
- Ligands
- ZN
- Released
- 6 Sept 2023
Explore 8IEJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IEJ contains 47 α-helices and 39 β-strands across 11 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: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 942-946 | 5 | |
| β-strand | 947 | 1 | 11 |
| β-strand | 955 | 1 | 11 |
| β-strand | 958-960 | 3 | 12 |
| β-strand | 966-967 | 2 | 12 |
| α-helix | 970-977 | 8 | |
| β-strand | 995-997 | 3 | 12 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 1 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 2 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 2 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 1 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 4 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 5 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 5 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 4 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 3 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-16 | 4 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 46-73 | 28 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 8 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 7 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 6 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain K: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 9 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 10 |
| α-helix | 121-131 | 11 | |
3 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 H2A type 1-B/E | C, G | protein | 109 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D | protein | 94 | Homo sapiens | O60814 (AlphaFold model) |
| Histone H3.1 | E, K | protein | 98 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | F, L | protein | 80 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2B type 1-K | H | protein | 94 | Homo sapiens | O60814 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Homo sapiens | |
| DNA (147-mer) | J | DNA | 147 | Homo sapiens | |
| E3 ubiquitin-protein ligase BRE1B | A | protein | 60 | Homo sapiens | O75150 |
| E3 ubiquitin-protein ligase BRE1A | M | protein | 60 | Homo sapiens | Q5VTR2 |
| Ubiquitin-conjugating enzyme E2 A | R | protein | 150 | Homo sapiens | P49459 |
Sequence of entity 1 (C, G), FASTA
>8IEJ_1 Histone H2A type 1-B/E (chains C, G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 2 (D), FASTA
>8IEJ_2 Histone H2B type 1-K (chains D)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSA
Sequence of entity 3 (E, K), FASTA
>8IEJ_3 Histone H3.1 (chains E, K)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAC
EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 4 (F, L), FASTA
>8IEJ_4 Histone H4 (chains F, L)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGFG
Sequence of entity 5 (H), FASTA
>8IEJ_5 Histone H2B type 1-K (chains H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 6 (I), FASTA
>8IEJ_6 DNA (147-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 7 (J), FASTA
>8IEJ_7 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT
Sequence of entity 8 (A), FASTA
>8IEJ_8 E3 ubiquitin-protein ligase BRE1B (chains A)
EYKARLTCPCCNTRKKDAVLTKCFHVFCFECVRGRYEARQRKCPKCNAAFGAHDFHRIYI
Sequence of entity 9 (M), FASTA
>8IEJ_9 E3 ubiquitin-protein ligase BRE1A (chains M)
DYKARLTCPCCNMRKKDAVLTKCFHVFCFECVKTRYDTRQRKCPKCNAAFGANDFHRIYI
Sequence of entity 10 (R), FASTA
>8IEJ_10 Ubiquitin-conjugating enzyme E2 A (chains R)
MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFT
EEYPNKPPTVRFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNS
PANSQAAQLYQENKREYEKRVSAIVEQSWR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Deng, Z., Ai, H., Sun, M. et al. Mol Cell (2023) 83:3080-3094.e14. DOI 10.1016/j.molcel.2023.08.001 · PubMed
Other PDB entries of the same protein (UniProt P04908 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7VZ4 1.89 Å, Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA…
- 6ACL 1.92 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95
- 8I17 1.98 Å, Structural basis for H2A-H2B recognitions by human Spt16
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 5Y0D 1.99 Å, Crystal Structure of the human nucleosome containing the H2B E76K mutant
- 6IPU 1.99 Å, Human nucleosome core particle containing 145 bp of DNA
- 8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
- 5Y0C 2.09 Å, Crystal Structure of the human nucleosome at 2.09 angstrom resolution
- 8Q3E 2.17 Å, High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
- 5X7X 2.18 Å, The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution
- 5AV6 2.2 Å, human nucleosome core particle
- 5AV8 2.2 Å, human nucleosome core particle
Browse structure collections
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