Research workbench
Cryo-EM structure of yeast mitochondrial RNA polymerase partially- melted transcription initiation complex (pmic)
Analyse Cryo-EM structure of yeast mitochondrial RNA polymerase partially- melted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMV
- Type
- protein + DNA
- Length
- 1,276 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial transcription factor 1; DNA-directed RNA polymerase, mitochondrial; DNA…
- EC
- 2.1.1.-, 2.7.7.6
- UniProt
- P14908, P13433
- Pockets
- 18 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mitochondrial transcription factor 1 (EC 2.1.1.-) | protein | 335 | 39% helix, 16% strand | P14908 |
| A | DNA-directed RNA polymerase, mitochondrial (EC 2.7.7.6) | protein | 887 | 52% helix, 11% strand | P13433 |
| N | DNA (33-mer) non-template | dna | 27 | — | — |
| T | DNA (33-mer) template | dna | 27 | — | — |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.81 | 0.82 | 87 | empty |
| 2 | 702 | 0.72 | 0.78 | 67 | empty |
| 3 | 463 | 0.69 | 0.80 | 51 | empty |
| 4 | 330 | 0.64 | 0.80 | 38 | empty |
| 5 | 202 | 0.63 | 0.84 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1564 Ų buried · 6 hydrogen bonds · protein-protein
- N–T · 1192 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–T · 648 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–N · 631 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–T · 472 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6YMV · Cryo-EM structure of yeast mitochondrial RNA polymerase partially-melted transcription… · 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 0.98
- 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 6YMV · PDBe 6YMV · UniProt P14908 · UniProt P13433
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