Research workbench
RNA polymerase II pre-initiation complex (PIC3)
Analyse RNA polymerase II pre-initiation complex (PIC3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ML2
- Type
- protein + DNA
- Length
- 8,315 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- A0A6A5Q1P2, A0A6A5Q4H2, A0A6A5Q0Z3, A0A6A5PTI6, A0A6A5Q456, A0A6L0ZRI7, A0A6A5Q270, A0A6A5Q8C2, A0A7I9EWC2, A0A6A5Q7Q6, A0A6A5Q7A1, A0A6A5PY05, P29055, P41895, A0A6A5PZ00, A0A6A5Q2T8, A0A6A5PRZ0, A0A6A5PTU5, A0A6A5PS93, G4XSG8, A0A6A5Q1C1, A0A6A5Q2X3, Q3E7C1, Q00578, A0A7I9BTI9
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 30 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1398 | 41% helix, 16% strand | A0A6A5Q1P2 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1152 | 29% helix, 23% strand | A0A6A5Q4H2 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 262 | 22% helix, 29% strand | A0A6A5Q0Z3 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 157 | 60% helix, 3% strand | A0A6A5PTI6 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 213 | 41% helix, 20% strand | A0A6A5Q456 |
| F | DNA-directed RNA polymerases I,II,AND III subunit RPABC2 | protein | 83 | 34% helix, 14% strand | A0A6L0ZRI7 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 8% helix, 49% strand | A0A6A5Q270 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 136 | 3% helix, 38% strand | A0A6A5Q8C2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 0% helix, 28% strand | A0A7I9EWC2 |
| J | DNA-directed RNA polymerases II subunit RPABC5 | protein | 65 | 45% helix, 2% strand | A0A6A5Q7Q6 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 112 | 35% helix, 20% strand | A0A6A5Q7A1 |
| L | DNA-directed RNA polymerases II subunit RPABC4 | protein | 45 | 0% helix, 11% strand | A0A6A5PY05 |
| M | Transcription initiation factor iib | protein | 279 | 51% helix, 4% strand | P29055 |
| Q | Transcription initiation factor iif subunit alpha | protein | 148 | 20% helix, 25% strand | P41895 |
| R | Transcription initiation factor iif subunit beta | protein | 190 | 29% helix, 21% strand | A0A6A5PZ00 |
| U | Transcription initiation factor iia large subunit | protein | 46 | 0% helix, 72% strand | A0A6A5Q2T8 |
| V | Transcription initiation factor iia subunit 2 | protein | 49 | 0% helix, 82% strand | A0A6A5PRZ0 |
| W | Transcription initiation factor iie subunit alpha | protein | 191 | 53% helix, 8% strand | A0A6A5PTU5 |
| X | Transcription initiation factor iie subunit beta | protein | 156 | 45% helix, 0% strand | A0A6A5PS93 |
| T | Template strand DNA | dna | 56 | — | — |
| N | Non-template strand DNA | dna | 56 | — | — |
| O | BJ4_G0004860.MRNA.1.CDS.1 | protein | 180 | 29% helix, 35% strand | G4XSG8 |
| 1 | TFB1 | protein | 367 | 63% helix, 0% strand | — |
| 4 | TFB4 | protein | 284 | 36% helix, 13% strand | — |
| 0 | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 754 | 49% helix, 10% strand | A0A6A5Q1C1 |
| 6 | General transcription and DNA repair factor iih | protein | 351 | 28% helix, 13% strand | — |
| 2 | RNA polymerase II transcription factor B subunit 2 | protein | 460 | 48% helix, 3% strand | A0A6A5Q2X3 |
| 5 | General transcription and DNA repair factor iih subunit TFB5 | protein | 66 | 47% helix, 24% strand | Q3E7C1 |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 634 | 36% helix, 10% strand | Q00578 |
| 3 | BJ4_G0050160.MRNA.1.CDS.1 | protein | 138 | 44% helix, 4% strand | A0A7I9BTI9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- ZN · Zinc ion · metal · 17 copies · chains A, B, C, I, J, L, M, W, 4, 6, 3
- MG · Magnesium ion · metal · chains 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 | 1182 | 0.87 | 0.87 | 148 | empty |
| 2 | 960 | 0.86 | 0.88 | 111 | empty |
| 3 | 1160 | 0.86 | 0.87 | 124 | empty |
| 4 | 1118 | 0.86 | 0.87 | 113 | empty |
| 5 | 929 | 0.86 | 0.87 | 116 | empty |
Interfaces
68 interfaces between chains.
- A–B · 9494 Ų buried · 119 hydrogen bonds · protein-protein
- T–N · 2573 Ų buried · 264 hydrogen bonds · nucleic-nucleic
- Q–R · 2249 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 2045 Ų buried · 31 hydrogen bonds · protein-protein
- A–M · 2014 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7ML2 · RNA polymerase II pre-initiation complex (PIC3) · 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 A0A6A5Q1P2
- Every structure of UniProt A0A6A5Q4H2
- Every structure of UniProt A0A6A5Q0Z3
- Every structure of UniProt A0A6A5PTI6
- Every structure of UniProt A0A6A5Q456
- Every structure of UniProt A0A6L0ZRI7
- Every structure of UniProt A0A6A5Q270
- Every structure of UniProt A0A6A5Q8C2
- Every structure of UniProt A0A7I9EWC2
- Every structure of UniProt A0A6A5Q7Q6
- Every structure of UniProt A0A6A5Q7A1
- Every structure of UniProt A0A6A5PY05
- Every structure of UniProt P29055
- Every structure of UniProt P41895
- Every structure of UniProt A0A6A5PZ00
- Every structure of UniProt A0A6A5Q2T8
- Every structure of UniProt A0A6A5PRZ0
- Every structure of UniProt A0A6A5PTU5
- Every structure of UniProt A0A6A5PS93
- Every structure of UniProt G4XSG8
- Every structure of UniProt A0A6A5Q1C1
- Every structure of UniProt A0A6A5Q2X3
- Every structure of UniProt Q3E7C1
- Every structure of UniProt Q00578
- Every structure of UniProt A0A7I9BTI9
- Elsewhere: RCSB PDB 7ML2 · PDBe 7ML2 · UniProt A0A6A5Q1P2 · UniProt A0A6A5Q4H2 · UniProt A0A6A5Q0Z3 · UniProt A0A6A5PTI6 · UniProt A0A6A5Q456 · UniProt A0A6L0ZRI7 · UniProt A0A6A5Q270 · UniProt A0A6A5Q8C2 · UniProt A0A7I9EWC2 · UniProt A0A6A5Q7Q6 · UniProt A0A6A5Q7A1 · UniProt A0A6A5PY05 · UniProt P29055 · UniProt P41895 · UniProt A0A6A5PZ00 · UniProt A0A6A5Q2T8 · UniProt A0A6A5PRZ0 · UniProt A0A6A5PTU5 · UniProt A0A6A5PS93 · UniProt G4XSG8 · UniProt A0A6A5Q1C1 · UniProt A0A6A5Q2X3 · UniProt Q3E7C1 · UniProt Q00578 · UniProt A0A7I9BTI9
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