Research workbench
The cryo-EM structure of cenp-a nucleosome in complex with the phosphorylated cenp-C
Analyse The cryo-EM structure of cenp-a nucleosome in complex with the phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BY0
- Type
- protein + DNA
- Length
- 1,154 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2,HISTONE H3-like centromeric protein a; Histone H4; Histone H2A type 1-B/E…
- UniProt
- Q6XXM1, P62805, P04908, P06899, O57393
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 56% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2,HISTONE H3-like centromeric protein a | protein | 103 | 62% helix, 1% strand | Q6XXM1 |
| B, F | Histone H4 | protein | 78 | 65% helix, 4% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 108 | 50% helix, 4% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 94 | 69% helix, 2% strand | P06899 |
| I | DNA (145-mer) | dna | 143 | — | — |
| J | DNA (145-mer) | dna | 143 | — | — |
| K, L | Maltose binding protein tag, LINKER,CENP-C | protein | 51 | 20% helix, 4% strand | O57393 |
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 | 919 | 0.88 | 0.90 | 116 | empty |
| 2 | 659 | 0.81 | 0.86 | 69 | empty |
| 3 | 98 | 0.77 | 0.97 | 22 | empty |
| 4 | 280 | 0.75 | 0.89 | 34 | empty |
| 5 | 408 | 0.74 | 0.84 | 49 | empty |
Interfaces
48 interfaces between chains.
- I–J · 6565 Ų buried · 679 hydrogen bonds · nucleic-nucleic
- A–B · 2470 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2468 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2439 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2343 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7BY0 · The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C · the same entry in another collection · chain L against L, TM-score 1.00
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 Q6XXM1
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt O57393
- Elsewhere: RCSB PDB 7BY0 · PDBe 7BY0 · UniProt Q6XXM1 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt O57393
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