8SMX
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2)
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 | C, G | Histone H2A type 1-B/E | polymer | 119 | 13008.2 | 2 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
4 | D, H | Histone H2B type 1-J | polymer | 128 | 14084.3 | 2 | UniProt (P06899) Pfam (PF00125) In PDB | Homo sapiens (human) | Histone H2B.1,Histone H2B.r,H2B/r |
5 | I | DNA (147-MER) | polymer | 147 | 45138.8 | 1 | Homo sapiens (human) | ||
6 | J | DNA (147-MER) | polymer | 147 | 45610.0 | 1 | Homo sapiens (human) | ||
7 | K | E3 ubiquitin-protein ligase RNF168 | polymer | 103 | 11904.0 | 1 | UniProt (Q8IYW5) Pfam (PF14447) In PDB | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
8 | L | Ubiquitin-conjugating enzyme E2 D3 | polymer | 151 | 17061.4 | 1 | UniProt (P61077) Pfam (PF00179) In PDB | Homo sapiens (human) | (E3-independent) E2 ubiquitin-conjugating enzyme D3,E2 ubiquitin-conjugating enzyme D3,Ubiquitin carrier protein D3,Ubiquitin-conjugating enzyme E2(17)KB 3,Ubiquitin-conjugating enzyme E2-17 kDa 3,Ubiquitin-protein ligase D3 |
9 | K | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, E: 0 - 135 (UniProt: P68431)
B, F: 0 - 102 (UniProt: P62805)
C, G: 11 - 129 (UniProt: P04908)
D, H: 0 - 123 (UniProt: P06899)
K: 1 - 93 (UniProt: Q8IYW5)
L: 1 - 147 (UniProt: P61077)
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 |
---|---|---|
Ser 11 | Arg 12 | engineered mutation |
Cys 15 | Lys 16 | engineered mutation |
PDB | External Database | Details |
---|---|---|
Gly -4 | - | expression tag |
Pro -3 | - | expression tag |
Gly -2 | - | expression tag |
His -1 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met -9 | - | expression tag |
Gly -8 | - | expression tag |
His -7 | - | expression tag |
His -6 | - | expression tag |
His -5 | - | expression tag |
His -4 | - | expression tag |
His -3 | - | expression tag |
His -2 | - | expression tag |
Gly -1 | - | expression tag |
Ser 0 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Gly -3 | - | expression tag |
Pro -2 | - | expression tag |
Gly -1 | - | expression tag |
His 0 | - | expression tag |
Ile 21 | Cys 21 | engineered mutation |
Ala 107 | Cys 107 | engineered mutation |
Asp 111 | Cys 111 | engineered mutation |
Lys 119 | Leu 119 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 12 |
Total formula weight | 228959.9 | |
Non-Polymers* | Number of molecules | 2 |
Total formula weight | 130.8 | |
All* | Total formula weight | 229090.7 |