Research workbench
Yeast RNA polymerase II transcription pre-initiation complex (consensus)
Analyse Yeast RNA polymerase II transcription pre-initiation complex (consensus) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4J
- Type
- protein + DNA
- Length
- 8,979 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcription and DNA repair factor iih helicase subunit xpd; General…
- EC
- 3.6.4.12, 2.7.7.6
- UniProt
- P06839, P32776, Q02939, Q03290, Q12004, Q3E7C1, Q04673, Q00578, P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145
- Ligands
- SF4, BEF, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 30 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 752 | 49% helix, 14% strand | P06839 |
| 1 | General transcription and DNA repair factor iih subunit TFB1 | protein | 522 | 57% helix, 10% strand | P32776 |
| 2 | General transcription and DNA repair factor iih subunit TFB2 | protein | 445 | 52% helix, 15% strand | Q02939 |
| 3 | RNA polymerase II transcription factor B subunit 3 | protein | 131 | 47% helix, 8% strand | Q03290 |
| 4 | General transcription and DNA repair factor iih subunit TFB4 | protein | 293 | 40% helix, 17% strand | Q12004 |
| 5 | General transcription and DNA repair factor iih subunit TFB5 | protein | 65 | 49% helix, 29% strand | Q3E7C1 |
| 6 | General transcription and DNA repair factor iih subunit SSL1 | protein | 356 | 32% helix, 20% strand | Q04673 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 615 | 39% helix, 17% strand | Q00578 |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1430 | 41% helix, 17% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1180 | 27% helix, 26% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 27% helix, 29% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 167 | 56% helix, 7% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 40% helix, 23% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 86 | 34% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 51% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 140 | 3% helix, 50% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 3% helix, 33% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 69 | 41% helix, 4% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 115 | 37% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 38% strand | P40422 |
| M | Transcription initiation factor iib | protein | 308 | 54% helix, 7% strand | P29055 |
| N | Non-template DNA | dna | 45 | — | — |
| O | Tata-box-binding protein | protein | 181 | 27% helix, 36% strand | P13393 |
| Q | Transcription initiation factor iif subunit alpha | protein | 221 | 29% helix, 25% strand | P41895 |
| R | Transcription initiation factor iif subunit beta (EC 3.6.4.12) | protein | 268 | 28% helix, 24% strand | P41896 |
| T | Template DNA | dna | 45 | — | — |
| U | Transcription initiation factor iia large subunit | protein | 107 | 39% helix, 37% strand | P32773 |
| V | Transcription initiation factor iia subunit 2 | protein | 104 | 39% helix, 38% strand | P32774 |
| W | Transcription initiation factor iie subunit alpha | protein | 312 | 49% helix, 11% strand | P36100 |
| X | Transcription initiation factor iie subunit beta | protein | 210 | 40% helix, 10% strand | P36145 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- BEF · Beryllium trifluoride ion · ligand · chains 7
- ADP · Adenosine-5'-diphosphate · ligand · chains 7
- ZN · Zinc ion · metal · 17 copies · chains 3, 4, 6, A, B, C, I, J, L, M, W
- MG · Magnesium ion · metal · 2 copies · chains 7, A
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 | 1103 | 0.88 | 0.90 | 139 | empty |
| 2 | 885 | 0.85 | 0.87 | 114 | empty |
| 3 | 1019 | 0.85 | 0.86 | 105 | empty |
| 4 | 1006 | 0.84 | 0.84 | 124 | empty |
| 5 | 217 | 0.83 | 0.97 | 33 | empty |
Interfaces
95 interfaces between chains.
- A–B · 9933 Ų buried · 140 hydrogen bonds · protein-protein
- 0–1 · 4150 Ų buried · 53 hydrogen bonds · protein-protein
- Q–R · 3516 Ų buried · 69 hydrogen bonds · protein-protein
- 1–4 · 3213 Ų buried · 32 hydrogen bonds · protein-protein
- B–Q · 2983 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7O4J · Yeast RNA polymerase II transcription pre-initiation complex (consensus) · the same entry in another collection · chain B against B, 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 P06839
- Every structure of UniProt P32776
- Every structure of UniProt Q02939
- Every structure of UniProt Q03290
- Every structure of UniProt Q12004
- Every structure of UniProt Q3E7C1
- Every structure of UniProt Q04673
- Every structure of UniProt Q00578
- Every structure of UniProt P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Every structure of UniProt P29055
- Every structure of UniProt P13393
- Every structure of UniProt P41895
- Every structure of UniProt P41896
- Every structure of UniProt P32773
- Every structure of UniProt P32774
- Every structure of UniProt P36100
- Every structure of UniProt P36145
- Elsewhere: RCSB PDB 7O4J · PDBe 7O4J · UniProt P06839 · UniProt P32776 · UniProt Q02939 · UniProt Q03290 · UniProt Q12004 · UniProt Q3E7C1 · UniProt Q04673 · UniProt Q00578 · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P29055 · UniProt P13393 · UniProt P41895 · UniProt P41896 · UniProt P32773 · UniProt P32774 · UniProt P36100 · UniProt P36145
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