6UH5
Structural basis of COMPASS eCM recognition of the H2Bub nucleosome
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E (A, E) | Histone H3 | polymer | 135 | 15275.9 | 2 | UniProt (Q92133) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 2 | B, F (B, F) | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 3 | C, G (C, G) | Histone H2A | polymer | 107 | 11694.6 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 4 | D (D) | Histone H2B | polymer | 125 | 13848.1 | 1 | UniProt (A0A1L8FQ56) Pfam (PF00125) UniProt (by SIFTS) (P02281) | Xenopus laevis (African clawed frog) | |
| 5 | H (H) | Histone H2B | polymer | 125 | 13822.1 | 1 | UniProt (A0A1L8FQ56) Pfam (PF00125) UniProt (by SIFTS) (P02281) | Xenopus laevis (African clawed frog) | |
| 6 | I (I) | DNA (146-MER) | polymer | 146 | 44825.6 | 1 | synthetic construct | ||
| 7 | J (J) | DNA (146-MER) | polymer | 146 | 45305.9 | 1 | synthetic construct | ||
| 8 | K (K) | Swd3 | polymer | 327 | 36458.9 | 1 | UniProt (Q6CLY5) Pfam (PF00400) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | |
| 9 | L (M) | Histone-lysine N-methyltransferase, H3 lysine-4 specific | polymer | 275 | 31448.5 | 1 | UniProt (Q6CIT4) Pfam (PF11764) Pfam (PF00856) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | COMPASS component SET1,SET domain-containing protein 1 |
| 10 | M (N) | Swd1 | polymer | 439 | 49894.7 | 1 | UniProt (Q6CXF3) Pfam (PF00400) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | |
| 11 | N (Q) | Ubiquitin | polymer | 76 | 8622.9 | 1 | UniProt (J3QS39) Pfam (PF00240) UniProt (by SIFTS) (P0CG47) | Homo sapiens (Human) | |
| 12 | O (R) | H3 N-terminus | polymer | 8 | 936.1 | 1 | UniProt (by SIFTS) (P84233) | Xenopus laevis (African clawed frog) | |
| 13 | P (X) | Spp1 | polymer | 342 | 39297.9 | 1 | UniProt (Q6CRQ4) Pfam (PF00628) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | |
| 14 | Q (L) | Bre2 | polymer | 405 | 47287.0 | 1 | UniProt (Q6CTQ1) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | |
| 15 | R, S (O, P) | Sdc1 | polymer | 134 | 14722.6 | 2 | UniProt (Q6CPN6) Pfam (PF05186) | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) | |
| 16 | T (M) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 17 | U (R) | S-ADENOSYLMETHIONINE | non-polymer | 398.4 | 1 | Chemie (SAM) |
Sequence modifications
D: -2 - 122 (UniProt: A0A1L8FQ56)
H: -2 - 122 (UniProt: A0A1L8FQ56)
M: 726 - 1000 (UniProt: Q6CIT4)
Q: 1 - 76 (UniProt: J3QS39)
| PDB | External Database | Details |
|---|---|---|
| Pro 7 | Ala 11 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Pro 7 | Ala 11 | conflict |
| Cys 117 | Lys 121 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Glu 761 | Asp 761 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Cys 76 | Gly 76 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 19 |
| Total formula weight | 437660.3 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 463.8 | |
| All* | Total formula weight | 438124.1 |
