Research workbench
Cryo-EM structure of nucleosome core particle
Analyse Cryo-EM structure of nucleosome core particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PWE
- Type
- protein + DNA
- Length
- 1,038 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (147-mer)
- UniProt
- P02299, A0A0B4KFZ9, P84051, P02283
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 49% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 96 | 42% helix, 2% strand | P02299 |
| B, F | Histone H4 | protein | 79 | 56% helix, 3% strand | A0A0B4KFZ9 |
| C, G | Histone H2A | protein | 103 | 46% helix, 4% strand | P84051 |
| D, H | Histone H2B | protein | 94 | 55% helix, 4% strand | P02283 |
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.79 | 0.81 | 102 | empty |
| 2 | 598 | 0.74 | 0.81 | 46 | empty |
| 3 | 777 | 0.71 | 0.77 | 52 | empty |
| 4 | 447 | 0.71 | 0.81 | 50 | empty |
| 5 | 305 | 0.69 | 0.84 | 31 | empty |
Interfaces
34 interfaces between chains.
- I–J · 6723 Ų buried · 672 hydrogen bonds · nucleic-nucleic
- C–D · 2662 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 2651 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2480 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2479 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6PWE · Cryo-EM structure of nucleosome core particle · the same entry in another collection · chain J against J, TM-score 1.00
- P02299 · AlphaFold monomer V2.0 prediction for histone H3 (P02299) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P84051 · AlphaFold monomer V2.0 prediction for histone H2A (P84051) · a predicted model of the same protein · chain C against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P02299
- Every structure of UniProt A0A0B4KFZ9
- Every structure of UniProt P84051
- Every structure of UniProt P02283
- Elsewhere: RCSB PDB 6PWE · PDBe 6PWE · UniProt P02299 · UniProt A0A0B4KFZ9 · UniProt P84051 · UniProt P02283
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