Research workbench
Cryo-EM structure of Substrate ATP Bound in the Insertion Site (IS) of Human Mitochondrial Transcription Elongation Complex
Analyse Cryo-EM structure of Substrate ATP Bound in the Insertion Site (IS) of Human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8U8V
- Type
- protein + DNA + RNA
- Length
- 1,453 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.74
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Transcription elongation factor, mitochondrial; DNA-directed RNA polymerase…
- UniProt
- Q96QE5, O00411
- Ligands
- APC, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 2.74 · 6 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription elongation factor, mitochondrial | protein | 202 | 41% helix, 15% strand | Q96QE5 |
| B | Transcription elongation factor, mitochondrial | protein | 200 | 39% helix, 16% strand | Q96QE5 |
| E | DNA-directed RNA polymerase, mitochondrial | protein | 990 | 52% helix, 8% strand | O00411 |
| N | Non-Template Strand DNA (NT27mt) | dna | 22 | — | — |
| R | RNA (RNA14mt) | rna | 9 | — | — |
| T | Template Strand DNA (TS31mt) | dna | 30 | — | — |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains E, R, T
- MG · Magnesium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.81 | 0.83 | 72 | APC, MG |
| 2 | 842 | 0.78 | 0.81 | 82 | empty |
| 3 | 225 | 0.77 | 0.91 | 38 | empty |
| 4 | 863 | 0.76 | 0.79 | 66 | empty |
| 5 | 472 | 0.75 | 0.84 | 57 | empty |
Interfaces
10 interfaces between chains.
- E–T · 1339 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 1169 Ų buried · 0 hydrogen bonds · protein-protein
- N–T · 901 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–E · 688 Ų buried · 3 hydrogen bonds · protein-protein
- E–R · 509 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- Q96QE5 · AlphaFold monomer V2.0 prediction for transcription elongation factor, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.96
- O00411 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase, mitochondrial (O00411) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 Q96QE5
- Every structure of UniProt O00411
- Elsewhere: RCSB PDB 8U8V · PDBe 8U8V · UniProt Q96QE5 · UniProt O00411
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