Research workbench
The cryo-EM structure of a. thaliana pol IV-RDR2 backtracked complex
Analyse The cryo-EM structure of a. thaliana pol IV-RDR2 backtracked complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EU0
- Type
- protein + DNA + RNA
- Length
- 4,249 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase IV subunit 1; DNA-directed RNA polymerases IV and V subunit…
- EC
- 2.7.7.6, 2.7.7.48
- UniProt
- Q9LK40, Q39211, O81098, Q9FJ98, Q9M1A8, Q6NLH0, Q8LFJ6, Q38859, Q9FLM8, O82504
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 15 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase IV subunit 1 | protein | 1060 | 33% helix, 16% strand | — |
| B | DNA-directed RNA polymerases IV and V subunit 2 (EC 2.7.7.6) | protein | 1054 | 25% helix, 22% strand | Q9LK40 |
| C | DNA-directed RNA polymerases II, IV and V subunit 3 | protein | 291 | 21% helix, 31% strand | Q39211 |
| E | DNA-directed RNA polymerases II and IV subunit 5A | protein | 198 | 32% helix, 20% strand | O81098 |
| F | DNA-directed RNA polymerases II, IV and V subunit 6A | protein | 76 | 36% helix, 16% strand | Q9FJ98 |
| H | DNA-directed RNA polymerases II, IV and V subunit 8B | protein | 126 | 0% helix, 40% strand | Q9M1A8 |
| I | DNA-directed RNA polymerases II, IV and V subunit 9A | protein | 113 | 0% helix, 37% strand | Q6NLH0 |
| J | DNA-directed RNA polymerases II, IV and V subunit 10 | protein | 62 | 47% helix, 5% strand | Q8LFJ6 |
| K | DNA-directed RNA polymerases II, IV and V subunit 11 | protein | 94 | 40% helix, 27% strand | Q38859 |
| L | DNA-directed RNA polymerases II, IV and V subunit 12 | protein | 42 | 0% helix, 33% strand | Q9FLM8 |
| M | RNA-dependent RNA polymerase 2 (EC 2.7.7.48) | protein | 1052 | 28% helix, 20% strand | O82504 |
| N | DNA (5'- D(*CP*TP*GP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*GP*AP*GP*TP*G)-3') | dna | 17 | — | — |
| O | RNA (39-mer) | rna | 32 | — | — |
| Q | DNA (33-mer) | dna | 28 | — | — |
| R | RNA (5'-R(*CP*CP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
- MG · Magnesium ion · metal · 2 copies · chains A, O, M, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1044 | 0.89 | 0.90 | 133 | empty |
| 2 | 826 | 0.87 | 0.90 | 109 | empty |
| 3 | 978 | 0.86 | 0.87 | 92 | empty |
| 4 | 1149 | 0.79 | 0.80 | 115 | empty |
| 5 | 829 | 0.77 | 0.81 | 72 | empty |
Interfaces
34 interfaces between chains.
- A–B · 8046 Ų buried · 82 hydrogen bonds · protein-protein
- A–I · 2390 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 1882 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1653 Ų buried · 17 hydrogen bonds · protein-protein
- B–J · 1476 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7EU0 · The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex · the same entry in another collection · chain M against M, 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 Q9LK40
- Every structure of UniProt Q39211
- Every structure of UniProt O81098
- Every structure of UniProt Q9FJ98
- Every structure of UniProt Q9M1A8
- Every structure of UniProt Q6NLH0
- Every structure of UniProt Q8LFJ6
- Every structure of UniProt Q38859
- Every structure of UniProt Q9FLM8
- Every structure of UniProt O82504
- Elsewhere: RCSB PDB 7EU0 · PDBe 7EU0 · UniProt Q9LK40 · UniProt Q39211 · UniProt O81098 · UniProt Q9FJ98 · UniProt Q9M1A8 · UniProt Q6NLH0 · UniProt Q8LFJ6 · UniProt Q38859 · UniProt Q9FLM8 · UniProt O82504
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