MolNFT v1 · #173471 · protein + DNA + RNA
Structure of a transcribing RNA polymerase II-U1 snrnp complex
7B0Y · DNA-directed RNA polymerase II subunit RPB1: “Structure of a transcribing RNA polymerase II-U1 snrnp complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #173471 on GenesisL1: 3D…
- PDB
- 7B0Y
- Type
- protein + DNA + RNA
- Length
- 5,019 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P11414, A0A0B8RVL1, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, I3LCB2, P60899, A0A4X1VYD0, F1RKE4, I3LN51, P08621, P09012, P62316, P62306, P62304, P62308, P62318, Q66K91, P62314
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 25 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1422 | 41% helix, 15% strand | P11414 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1131 | 29% helix, 24% strand | A0A0B8RVL1 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 260 | 22% helix, 25% strand | I3LCH3 |
| D | DNA-directed RNA polymerase II subunit D | protein | 126 | 60% helix, 3% strand | A0A287ADR4 |
| E | DNA-directed RNA polymerase II subunit E | protein | 209 | 39% helix, 25% strand | I3LSI7 |
| F | DNA-directed RNA polymerase II subunit F | protein | 82 | 33% helix, 16% strand | F1SKN8 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 52% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 2% helix, 47% strand | I3LCB2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 117 | 7% helix, 30% strand | P60899 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 67 | 40% helix, 4% strand | A0A4X1VYD0 |
| K | DNA-directed RNA polymerase II subunit RPB11-a | protein | 115 | 42% helix, 22% strand | F1RKE4 |
| L | RPB12 | protein | 46 | 0% helix, 24% strand | I3LN51 |
| N | Non-template DNA | dna | 37 | — | — |
| P | 145-nt RNA | rna | 36 | — | — |
| T | Template DNA | dna | 37 | — | — |
| a | U1 snrna | rna | 164 | — | — |
| b | U1 small nuclear ribonucleoprotein 70 kda | protein | 186 | 25% helix, 16% strand | P08621 |
| c | U1 small nuclear ribonucleoprotein a | protein | 98 | 34% helix, 24% strand | P09012 |
| e | Small nuclear ribonucleoprotein sm D2 | protein | 95 | 18% helix, 42% strand | P62316 |
| f | Small nuclear ribonucleoprotein F | protein | 74 | 9% helix, 55% strand | P62306 |
| g | Small nuclear ribonucleoprotein E | protein | 77 | 14% helix, 55% strand | P62304 |
| h | Small nuclear ribonucleoprotein G | protein | 73 | 0% helix, 42% strand | P62308 |
| i | Small nuclear ribonucleoprotein sm D3 | protein | 81 | 16% helix, 46% strand | P62318 |
| j | Small nuclear ribonucleoprotein-associated protein | protein | 86 | 8% helix, 47% strand | Q66K91 |
| k | Small nuclear ribonucleoprotein sm D1 | protein | 81 | 10% helix, 46% strand | P62314 |
Ligands and binding sites
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 | 1120 | 0.87 | 0.88 | 141 | empty |
| 2 | 913 | 0.86 | 0.88 | 82 | empty |
| 3 | 426 | 0.84 | 0.92 | 50 | empty |
| 4 | 592 | 0.83 | 0.88 | 68 | empty |
| 5 | 722 | 0.81 | 0.85 | 83 | empty |
Interfaces
62 interfaces between chains.
- A–B · 9266 Ų buried · 132 hydrogen bonds · protein-protein
- A–E · 2455 Ų buried · 36 hydrogen bonds · protein-protein
- a–b · 2262 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–H · 2261 Ų buried · 28 hydrogen bonds · protein-protein
- C–K · 2245 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7B0Y · Structure of a transcribing RNA polymerase II-U1 snRNP complex · the same entry in another collection · chain K against K, 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 P11414
- Every structure of UniProt A0A0B8RVL1
- Every structure of UniProt I3LCH3
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LJZ9
- Every structure of UniProt I3LCB2
- Every structure of UniProt P60899
- Every structure of UniProt A0A4X1VYD0
- Every structure of UniProt F1RKE4
- Every structure of UniProt I3LN51
- Every structure of UniProt P08621
- Every structure of UniProt P09012
- Every structure of UniProt P62316
- Every structure of UniProt P62306
- Every structure of UniProt P62304
- Every structure of UniProt P62308
- Every structure of UniProt P62318
- Every structure of UniProt Q66K91
- Every structure of UniProt P62314
- Elsewhere: RCSB PDB 7B0Y · PDBe 7B0Y · UniProt P11414 · UniProt A0A0B8RVL1 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt I3LCB2 · UniProt P60899 · UniProt A0A4X1VYD0 · UniProt F1RKE4 · UniProt I3LN51 · UniProt P08621 · UniProt P09012 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P62318 · UniProt Q66K91 · UniProt P62314
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