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Cryo-EM structure of mouse RAG1/2 hfc complex containing partial HMGB1 LINKER(3.9 a)
Analyse Cryo-EM structure of mouse RAG1/2 hfc complex containing partial HMGB1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIJ
- Type
- protein + DNA
- Length
- 2,257 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V(D)J recombination-activating protein 1; DNA (46-mer); DNA…
- EC
- 3.1.-.-, 2.3.2.27
- UniProt
- P15919, P09429, P21784
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 614 | 49% helix, 10% strand | P15919 |
| C | V(D)J recombination-activating protein 1 (EC 3.1.-.-, 2.3.2.27) | protein | 616 | 49% helix, 11% strand | P15919 |
| F | DNA (46-mer) | dna | 46 | — | — |
| I | DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)- 3') | dna | 16 | — | — |
| J | DNA (5'- D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3') | dna | 19 | — | — |
| G | DNA (60-mer) | dna | 60 | — | — |
| N | High mobility group protein B1 | protein | 133 | 58% helix, 0% strand | P09429 |
| L | DNA (30-mer) | dna | 30 | — | — |
| D | V(D)J recombination-activating protein 2 | protein | 340 | 2% helix, 40% strand | P21784 |
| B | V(D)J recombination-activating protein 2 | protein | 342 | 2% helix, 39% strand | P21784 |
| M | DNA (41-mer) | dna | 41 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A, F, C, J, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1057 | 0.86 | 0.87 | 90 | empty |
| 2 | 1058 | 0.83 | 0.84 | 95 | empty |
| 3 | 604 | 0.83 | 0.88 | 58 | empty |
| 4 | 812 | 0.83 | 0.85 | 68 | empty |
| 5 | 344 | 0.80 | 0.90 | 50 | empty |
Interfaces
27 interfaces between chains.
- A–C · 3920 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2064 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2007 Ų buried · 35 hydrogen bonds · protein-protein
- G–M · 1827 Ų buried · 144 hydrogen bonds · nucleic-nucleic
- F–L · 1325 Ų buried · 95 hydrogen bonds · nucleic-nucleic
Compared structures
- 6CIJ · Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) · the same entry in another collection · chain M against M, TM-score 1.00
- P15919 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (P15919) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P15919
- Every structure of UniProt P09429
- Every structure of UniProt P21784
- Elsewhere: RCSB PDB 6CIJ · PDBe 6CIJ · UniProt P15919 · UniProt P09429 · UniProt P21784
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