MolNFT v1 · #170912 · protein + DNA + RNA
Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex
6YMW · Mitochondrial transcription factor 1: “Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex”. Electron microscopy, 2 ligands (P5E, MG), 17 pockets (best druggability 0.84). MolNFT v1 #170912 on…
- PDB
- 6YMW
- Type
- protein + DNA + RNA
- Length
- 1,313 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial transcription factor 1; DNA-directed RNA polymerase, mitochondrial; Chains…
- EC
- 2.1.1.-, 2.7.7.6
- UniProt
- P14908, P13433
- Ligands
- P5E, MG
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mitochondrial transcription factor 1 (EC 2.1.1.-) | protein | 340 | 38% helix, 15% strand | P14908 |
| A | DNA-directed RNA polymerase, mitochondrial (EC 2.7.7.6) | protein | 913 | 53% helix, 11% strand | P13433 |
| N | Chains: N | dna | 29 | — | — |
| T | Chains: T | dna | 29 | — | — |
| C | RNA (pppgpg) | rna | 2 | — | — |
Ligands and binding sites
- P5E · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene) pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, T, C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.84 | 0.85 | 101 | empty |
| 2 | 810 | 0.82 | 0.85 | 84 | P5E, MG |
| 3 | 834 | 0.81 | 0.84 | 70 | empty |
| 4 | 1036 | 0.73 | 0.77 | 78 | empty |
| 5 | 277 | 0.71 | 0.86 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1887 Ų buried · 8 hydrogen bonds · protein-protein
- A–T · 1580 Ų buried · 31 hydrogen bonds · protein-nucleic
- N–T · 1077 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- A–N · 1013 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–N · 619 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6YMW · Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex · the same entry in another collection · chain B against B, TM-score 1.00
- P14908 · AlphaFold monomer V2.0 prediction for mitochondrial transcription factor 1 (P14908) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P13433 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase, mitochondrial (P13433) · a predicted model of the same protein · chain A 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 P14908
- Every structure of UniProt P13433
- Elsewhere: RCSB PDB 6YMW · PDBe 6YMW · UniProt P14908 · UniProt P13433
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