8DU4: Histone H3
Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome. Determined by electron microscopy at 3.55 Å resolution. Released 21 Sept 2022.
- Method
- Electron microscopy
- Resolution
- 3.55 Å
- Organisms
- Xenopus laevis, synthetic construct, Homo sapiens
- Chains
- 13
- Atoms
- 17,407
- Mol. weight
- 304.2 kDa
- Released
- 21 Sept 2022
Explore 8DU4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DU4 contains 41 α-helices and 82 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| α-helix | 64-74 | 11 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 88-113 | 26 | |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| α-helix | 51-75 | 25 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 98 | 1 | 2 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 3 |
| α-helix | 47-73 | 27 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 5 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-45 | 10 | |
| β-strand | 50-51 | 2 | 4 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 3 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 83 | 1 | 6 |
| α-helix | 88-113 | 26 | |
| β-strand | 119 | 1 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 46 | 1 | 7 |
| α-helix | 51-74 | 24 | |
| β-strand | 80 | 1 | 6 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-98 | 2 | 5 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-19 | 3 | |
| α-helix | 28-35 | 8 | |
| α-helix | 47-73 | 27 | |
| β-strand | 77 | 1 | 8 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 102 | 1 | 2 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-45 | 10 | |
| β-strand | 50 | 1 | 8 |
| α-helix | 53-80 | 28 | |
| α-helix | 89-98 | 10 | |
| α-helix | 101-120 | 20 | |
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 H3 | A, E | protein | 136 | Xenopus laevis | P02302 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| 601 DNA (146-mer) | I | DNA | 146 | synthetic construct | |
| 601 DNA (146-mer) | J | DNA | 146 | synthetic construct | |
| WD repeat-containing protein 5 | L | protein | 335 | Homo sapiens | P61964 |
| Retinoblastoma-binding protein 5 | N | protein | 538 | Homo sapiens | Q15291 |
| Polyubiquitin-B | O | protein | 81 | Homo sapiens | P0CG47 |
Sequence of entity 1 (A, E), FASTA
>8DU4_1 Histone H3 (chains A, E)
MARTLQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVALFEDTNLCAIHAKRVTI
LPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8DU4_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8DU4_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>8DU4_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYT
SAK
Sequence of entity 5 (I), FASTA
>8DU4_5 601 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>8DU4_6 601 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA
Sequence of entity 7 (L), FASTA
>8DU4_7 WD repeat-containing protein 5 (chains L)
GSATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEW
LASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSG
KCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLK
LWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQG
HTDVVISTACHPTENIIASAALENDKTIKLWKSDC
Sequence of entity 8 (N), FASTA
>8DU4_8 Retinoblastoma-binding protein 5 (chains N)
MNLELLESFGQNYPEEADGTLDCISMALTCTFNRWGTLLAVGCNDGRIVIWDFLTRGIAK
IISAHIHPVCSLCWSRDGHKLVSASTDNIVSQWDVLSGDCDQRFRFPSPILKVQYHPRDQ
NKVLVCPMKSAPVMLTLSDSKHVVLPVDDDSDLNVVASFDRRGEYIYTGNAKGKILVLKT
DSQDLVASFRVTTGTSNTTAIKSIEFARKGSCFLINTADRIIRVYDGREILTCGRDGEPE
PMQKLQDLVNRTPWKKCCFSGDGEYIVAGSARQHALYIWEKSIGNLVKILHGTRGELLLD
VAWHPVRPIIASISSGVVSIWAQNQVENWSAFAPDFKELDENVEYEERESEFDIEDEDKS
EPEQTGADAAEDEEVDVTSVDPIAAFCSSDEELEDSKALLYLPIAPEVEDPEENPYGPPP
DAVQTSLMDEGASSEKKRQSSADGSQPPKKKPKTTNIELQGVPNDEVHPLLGVKGDGKSK
KKQAGRPKGSKGKEKDSPFKPKLYKGDRGLPLEGSAKGKVQAELSQPLTAGGAISELL
Sequence of entity 9 (O), FASTA
>8DU4_9 Polyubiquitin-B (chains O)
QGSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGC
Primary citation
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Rahman, S., Hoffmann, N.A., Worden, E.J. et al. Proc Natl Acad Sci U S A (2022) 119:e2205691119-e2205691119. DOI 10.1073/pnas.2205691119 · PubMed
Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
- 1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 1AOI 2.8 Å, Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment
- 8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
- 8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
- 8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
- 6PX1 3.3 Å, Set2 bound to nucleosome
- 7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
- 6NZO 3.8 Å, Set2 bound to nucleosome
- 6PX3 4.1 Å, Set2 bound to nucleosome
Browse structure collections
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