MolNFT v2 · #214354 · protein + DNA
Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant
8JLB · Histone H3.2: “Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant”. Electron microscopy at 2.36, 20 pockets (best druggability 0.76). MolNFT v2 #214354 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8JLB
- Type
- protein + DNA
- Length
- 1,036 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.36
- Source
- Homo sapiens; synthetic construct
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (145-mer)
- UniProt
- Q71DI3, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · resolution 2.36 · 6 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 95 | 67% helix, 4% strand | Q71DI3 |
| B, F | Histone H4 | protein | 78 | 63% helix, 9% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 107 | 55% helix, 7% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 93 | 73% helix, 4% strand | P06899 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.76 | 0.83 | 59 | empty |
| 2 | 311 | 0.72 | 0.86 | 45 | empty |
| 3 | 382 | 0.72 | 0.84 | 40 | empty |
| 4 | 245 | 0.72 | 0.87 | 33 | empty |
| 5 | 208 | 0.70 | 0.87 | 33 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6524 Ų buried · 479 hydrogen bonds · nucleic-nucleic
- C–D · 2620 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2612 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2492 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2489 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain H against A, TM-score 0.99
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P04908 · AlphaFold monomer V2.0 prediction for histone H2A type 1-B/E (P04908) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 8JLB · PDBe 8JLB · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt P06899
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