Research workbench
RNA polymerase II initially transcribing complex (itc)
Analyse RNA polymerase II initially transcribing complex (itc) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ML4
- Type
- protein + DNA + RNA
- Length
- 8,119 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor iif subunit alpha; Transcription initiation factor iif…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- P41895, A0A6A5PZ00, A0A6A5PTI6, A0A6A5Q270, P29055, A0A6A5Q1P2, A0A6A5Q4H2, A0A6A5Q0Z3, A0A6A5Q456, A0A6L0ZRI7, A0A6A5Q8C2, A0A7I9EWC2, A0A6A5Q7Q6, A0A6A5Q7A1, A0A6A5PY05, A0A7I9BTI9, A0A6A5Q1C1, A0A7I9C5C2, A0A7I9FQL5, Q00578, Q3E7C1, A0A6A5Q2X3, A0A6A5PS93, A0A6A5Q2T8, A0A6A5PRZ0, P13393, A0A6A5PTU5
- Ligands
- SF4, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 31 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | Transcription initiation factor iif subunit alpha | protein | 148 | 19% helix, 21% strand | P41895 |
| R | Transcription initiation factor iif subunit beta | protein | 154 | 31% helix, 29% strand | A0A6A5PZ00 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 157 | 60% helix, 3% strand | A0A6A5PTI6 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 44% strand | A0A6A5Q270 |
| M | Transcription initiation factor iib | protein | 234 | 56% helix, 6% strand | P29055 |
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1405 | 40% helix, 14% strand | A0A6A5Q1P2 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 29% helix, 22% strand | A0A6A5Q4H2 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 27% strand | A0A6A5Q0Z3 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 41% helix, 22% strand | A0A6A5Q456 |
| F | DNA-directed RNA polymerases I,II,AND III subunit RPABC2 | protein | 85 | 31% helix, 2% strand | A0A6L0ZRI7 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 2% helix, 38% strand | A0A6A5Q8C2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 3% helix, 24% strand | A0A7I9EWC2 |
| J | DNA-directed RNA polymerases II subunit RPABC5 | protein | 65 | 49% helix, 0% strand | A0A6A5Q7Q6 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 39% helix, 22% strand | A0A6A5Q7A1 |
| L | DNA-directed RNA polymerases II subunit RPABC4 | protein | 46 | 0% helix, 24% strand | A0A6A5PY05 |
| 3 | BJ4_G0050160.MRNA.1.CDS.1 | protein | 72 | 75% helix, 0% strand | A0A7I9BTI9 |
| 0 | General transcription and DNA repair factor iih helicase subunit xpd (EC 3.6.4.12) | protein | 754 | 48% helix, 9% strand | A0A6A5Q1C1 |
| 4 | General transcription and DNA repair factor iih subunit TFB4 | protein | 284 | 37% helix, 13% strand | A0A7I9C5C2 |
| 6 | General transcription and DNA repair factor iih | protein | 351 | 28% helix, 15% strand | A0A7I9FQL5 |
| 1 | TFB1 | protein | 367 | 61% helix, 0% strand | — |
| 7 | General transcription and DNA repair factor iih helicase subunit xpb (EC 3.6.4.12) | protein | 634 | 38% helix, 11% strand | Q00578 |
| 5 | General transcription and DNA repair factor iih subunit TFB5 | protein | 66 | 42% helix, 21% strand | Q3E7C1 |
| 2 | RNA polymerase II transcription factor B subunit 2 | protein | 460 | 48% helix, 4% strand | A0A6A5Q2X3 |
| X | Transcription initiation factor iie subunit beta | protein | 149 | 41% helix, 0% strand | A0A6A5PS93 |
| U | Transcription initiation factor iia large subunit | protein | 46 | 0% helix, 54% strand | A0A6A5Q2T8 |
| V | Transcription initiation factor iia subunit 2 | protein | 49 | 0% helix, 78% strand | A0A6A5PRZ0 |
| N | Non-template strand DNA | dna | 38 | — | — |
| T | Template strand DNA | dna | 48 | — | — |
| O | Tata-box-binding protein | protein | 180 | 26% helix, 38% strand | P13393 |
| W | Transcription initiation factor iie subunit alpha | protein | 191 | 53% helix, 12% strand | A0A6A5PTU5 |
| P | RNA | rna | 5 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains 0
- ZN · Zinc ion · metal · 15 copies · chains M, A, B, C, Q, I, J, L, 4, 6, W
- MG · Magnesium ion · metal · chains A, P
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 | 995 | 0.88 | 0.89 | 111 | empty |
| 2 | 1095 | 0.85 | 0.86 | 103 | empty |
| 3 | 967 | 0.85 | 0.86 | 94 | empty |
| 4 | 726 | 0.85 | 0.88 | 95 | empty |
| 5 | 1062 | 0.84 | 0.85 | 139 | empty |
Interfaces
72 interfaces between chains.
- A–B · 9166 Ų buried · 143 hydrogen bonds · protein-protein
- 0–1 · 2765 Ų buried · 30 hydrogen bonds · protein-protein
- 4–6 · 2324 Ų buried · 20 hydrogen bonds · protein-protein
- Q–R · 2175 Ų buried · 49 hydrogen bonds · protein-protein
- C–K · 2099 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7ML4 · RNA polymerase II initially transcribing complex (ITC) · the same entry in another collection · chain H against H, 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 P41895
- Every structure of UniProt A0A6A5PZ00
- Every structure of UniProt A0A6A5PTI6
- Every structure of UniProt A0A6A5Q270
- Every structure of UniProt P29055
- Every structure of UniProt A0A6A5Q1P2
- Every structure of UniProt A0A6A5Q4H2
- Every structure of UniProt A0A6A5Q0Z3
- Every structure of UniProt A0A6A5Q456
- Every structure of UniProt A0A6L0ZRI7
- 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 A0A7I9BTI9
- Every structure of UniProt A0A6A5Q1C1
- Every structure of UniProt A0A7I9C5C2
- Every structure of UniProt A0A7I9FQL5
- Every structure of UniProt Q00578
- Every structure of UniProt Q3E7C1
- Every structure of UniProt A0A6A5Q2X3
- Every structure of UniProt A0A6A5PS93
- Every structure of UniProt A0A6A5Q2T8
- Every structure of UniProt A0A6A5PRZ0
- Every structure of UniProt P13393
- Every structure of UniProt A0A6A5PTU5
- Elsewhere: RCSB PDB 7ML4 · PDBe 7ML4 · UniProt P41895 · UniProt A0A6A5PZ00 · UniProt A0A6A5PTI6 · UniProt A0A6A5Q270 · UniProt P29055 · UniProt A0A6A5Q1P2 · UniProt A0A6A5Q4H2 · UniProt A0A6A5Q0Z3 · UniProt A0A6A5Q456 · UniProt A0A6L0ZRI7 · UniProt A0A6A5Q8C2 · UniProt A0A7I9EWC2 · UniProt A0A6A5Q7Q6 · UniProt A0A6A5Q7A1 · UniProt A0A6A5PY05 · UniProt A0A7I9BTI9 · UniProt A0A6A5Q1C1 · UniProt A0A7I9C5C2 · UniProt A0A7I9FQL5 · UniProt Q00578 · UniProt Q3E7C1 · UniProt A0A6A5Q2X3 · UniProt A0A6A5PS93 · UniProt A0A6A5Q2T8 · UniProt A0A6A5PRZ0 · UniProt P13393 · UniProt A0A6A5PTU5
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