8U13
Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1)
Entity
Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
1 | A, E | Histone H3.1 | polymer | 140 | 15786.5 | 2 | UniProt (P68431) Pfam (PF00125) In PDB | Homo sapiens (human) | Histone H3/a,Histone H3/b,Histone H3/c,Histone H3/d,Histone H3/f,Histone H3/h,Histone H3/i,Histone H3/j,Histone H3/k,Histone H3/l |
2 | B, F | Histone H4 | polymer | 107 | 11743.8 | 2 | UniProt (P62805) Pfam (PF15511) In PDB | Homo sapiens (human) | |
3 | D, H | Histone H2B type 1-C/E/F/G/I | polymer | 128 | 14084.3 | 2 | UniProt (P62807) Pfam (PF00125) In PDB | Homo sapiens (human) | Histone H2B.1 A,Histone H2B.a,H2B/a,Histone H2B.g,H2B/g,Histone H2B.h,H2B/h,Histone H2B.k,H2B/k,Histone H2B.l,H2B/l |
4 | I | DNA (147-MER) | polymer | 147 | 45138.8 | 1 | Homo sapiens (human) | ||
5 | J | DNA (146-MER) | polymer | 147 | 45610.0 | 1 | Homo sapiens (human) | ||
6 | K | E3 ubiquitin-protein ligase RNF168 | polymer | 99 | 11175.1 | 1 | UniProt (Q8IYW5) Pfam (PF14447) In PDB | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
7 | C, G | Histone H2A type 1-B/E | polymer | 119 | 12992.1 | 2 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
8 | K | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, E: 0 - 135 (UniProt: P68431)
B, F: 0 - 102 (UniProt: P62805)
D, H: 0 - 123 (UniProt: P62807)
K: 1 - 94 (UniProt: Q8IYW5)
C, G: 12 - 129 (UniProt: P04908)
PDB | External Database | Details |
---|---|---|
Gly -4 | - | expression tag |
Pro -3 | - | expression tag |
Gly -2 | - | expression tag |
His -1 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Gly -4 | - | expression tag |
Pro -3 | - | expression tag |
Gly -2 | - | expression tag |
His -1 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Gly -4 | - | expression tag |
Pro -3 | - | expression tag |
Gly -2 | - | expression tag |
His -1 | - | expression tag |
Ile 39 | Val 40 | conflict |
PDB | External Database | Details |
---|---|---|
Ser 95 | - | expression tag |
Gly 96 | - | expression tag |
Ser 97 | - | expression tag |
Gly 98 | - | expression tag |
Ser 99 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Ser 11 | - | expression tag |
Ser 13 | Lys 14 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 11 |
Total formula weight | 211137.4 | |
Non-Polymers* | Number of molecules | 2 |
Total formula weight | 130.8 | |
All* | Total formula weight | 211268.3 |