6P1H
Cryo-EM Structure of DNA Polymerase Delta Holoenzyme
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A | DNA polymerase delta catalytic subunit | polymer | 1119 | 127438.2 | 1 | UniProt (P15436) Pfam (PF03104) Pfam (PF00136) Pfam (PF14260) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | DNA polymerase III |
| 2 | B | DNA polymerase delta small subunit | polymer | 494 | 55987.4 | 1 | UniProt (P46957) Pfam (PF18018) Pfam (PF04042) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Hydroxyurea-sensitive protein 2 |
| 3 | C | DNA polymerase delta subunit 3 | polymer | 350 | 40377.7 | 1 | UniProt (P47110) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 4 | P, T | DNA (30-MER) | polymer | 30 | 9248.0 | 2 | synthetic construct | ||
| 5 | A | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 1 | Chemie (SF4) | |||
| 6 | A | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE | non-polymer | 467.2 | 1 | Chemie (DCP) | |||
| 7 | A, T | CALCIUM ION | non-polymer | 40.1 | 5 | Chemie (CA) | |||
| 8 | water | water | 18.0 | 44 | Chemie (HOH) |
Sequence modifications
A: 1 - 1097 (UniProt: P15436)
B: 1 - 487 (UniProt: P46957)
| PDB | External Database | Details |
|---|---|---|
| Met -21 | - | initiating methionine |
| Asp -20 | - | expression tag |
| Tyr -19 | - | expression tag |
| Lys -18 | - | expression tag |
| Asp -17 | - | expression tag |
| Asp -16 | - | expression tag |
| Asp -15 | - | expression tag |
| Asp -14 | - | expression tag |
| Lys -13 | - | expression tag |
| Gly -12 | - | expression tag |
| Asp -11 | - | expression tag |
| His -10 | - | expression tag |
| Asn -9 | - | expression tag |
| His -8 | - | expression tag |
| Arg -7 | - | expression tag |
| His -6 | - | expression tag |
| Lys -5 | - | expression tag |
| His -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Asp -2 | - | expression tag |
| Pro -1 | - | expression tag |
| His 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -6 | - | expression tag |
| Pro -5 | - | expression tag |
| Gly -4 | - | expression tag |
| Gly -3 | - | expression tag |
| Asp -2 | - | expression tag |
| Leu -1 | - | expression tag |
| His 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 5 |
| Total formula weight | 242299.2 | |
| Non-Polymers* | Number of molecules | 7 |
| Total formula weight | 1019.2 | |
| All* | Total formula weight | 243318.4 |
