MolNFT v1 · #153150 · protein + DNA + RNA
RNA polymerase II elongation complex bound with SPT4/5 and foreign DNA, stalled at shl(-1) of the nucleosome, weak ELF1 (+1 position)
6J51 · DNA-directed RNA polymerase subunit: “RNA polymerase II elongation complex bound with SPT4/5 and foreign DNA, stalled at shl(-1) of the nucleosome…”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88).…
- PDB
- 6J51
- Type
- protein + DNA + RNA
- Length
- 5,459 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
- EC
- 2.7.7.6
- UniProt
- C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, C4QZ45, C4R0E6, C4R370, P84243, P62805, P04908, P06899
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 28 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1411 | 42% helix, 17% strand | C4R4Y0 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1157 | 27% helix, 25% strand | C4QZQ7 |
| C | RNA polymerase II third largest subunit B44, part of central core | protein | 263 | 25% helix, 30% strand | C4R7L2 |
| D | RNA polymerase II subunit B32 | protein | 168 | 51% helix, 8% strand | C4R2U9 |
| E | RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III | protein | 213 | 40% helix, 24% strand | C4R3P8 |
| F | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | protein | 84 | 35% helix, 17% strand | C4R1V1 |
| G | RNA polymerase II subunit | protein | 171 | 13% helix, 49% strand | C4R9A1 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 8% helix, 49% strand | C4R273 |
| I | DNA-directed RNA polymerase subunit | protein | 111 | 3% helix, 32% strand | F2QPE6 |
| J | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | protein | 66 | 44% helix, 5% strand | C4R009 |
| K | RNA polymerase II subunit B12.5 | protein | 113 | 41% helix, 24% strand | C4R3Z5 |
| L | RNA polymerase subunit ABC10-alpha | protein | 45 | 0% helix, 29% strand | F2QMI1 |
| P | RNA (5'- R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3') | rna | 16 | — | — |
| T | DNA (198-mer) | dna | 127 | — | — |
| N | DNA (198-mer) | dna | 122 | — | — |
| M | Transcription elongation factor 1 homolog | protein | 64 | 19% helix, 36% strand | C4QZ45 |
| V | Transcription elongation factor SPT4 | protein | 102 | 30% helix, 22% strand | C4R0E6 |
| W | Protein that forms a complex with SPT4P | protein | 275 | 19% helix, 32% strand | C4R370 |
| a | Histone H3.3 | protein | 97 | 64% helix, 3% strand | P84243 |
| b | Histone H4 | protein | 80 | 64% helix, 5% strand | P62805 |
| c | Histone H2A type 1-B/E | protein | 103 | 57% helix, 3% strand | P04908 |
| d | Histone H2B type 1-J | protein | 95 | 73% helix, 2% strand | P06899 |
| e | Histone H3.3 | protein | 97 | 63% helix, 3% strand | P84243 |
| f | Histone H4 | protein | 78 | 65% helix, 5% strand | P62805 |
| g | Histone H2A type 1-B/E | protein | 105 | 52% helix, 5% strand | P04908 |
| h | Histone H2B type 1-J | protein | 91 | 78% helix, 4% strand | P06899 |
| 0 | DNA (36-mer) | dna | 36 | — | — |
| 1 | DNA (36-mer) | dna | 36 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, I, J, L, M, V
- 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 | 770 | 0.88 | 0.91 | 101 | empty |
| 2 | 913 | 0.85 | 0.87 | 88 | empty |
| 3 | 967 | 0.84 | 0.85 | 90 | empty |
| 4 | 961 | 0.84 | 0.85 | 115 | empty |
| 5 | 721 | 0.83 | 0.87 | 63 | empty |
Interfaces
90 interfaces between chains.
- A–B · 10138 Ų buried · 109 hydrogen bonds · protein-protein
- T–N · 5338 Ų buried · 539 hydrogen bonds · nucleic-nucleic
- a–b · 2481 Ų buried · 16 hydrogen bonds · protein-protein
- c–d · 2457 Ų buried · 14 hydrogen bonds · protein-protein
- e–f · 2419 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6J51 · RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at… · 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 C4R4Y0
- Every structure of UniProt C4QZQ7
- Every structure of UniProt C4R7L2
- Every structure of UniProt C4R2U9
- Every structure of UniProt C4R3P8
- Every structure of UniProt C4R1V1
- Every structure of UniProt C4R9A1
- Every structure of UniProt C4R273
- Every structure of UniProt F2QPE6
- Every structure of UniProt C4R009
- Every structure of UniProt C4R3Z5
- Every structure of UniProt F2QMI1
- Every structure of UniProt C4QZ45
- Every structure of UniProt C4R0E6
- Every structure of UniProt C4R370
- Every structure of UniProt P84243
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6J51 · PDBe 6J51 · UniProt C4R4Y0 · UniProt C4QZQ7 · UniProt C4R7L2 · UniProt C4R2U9 · UniProt C4R3P8 · UniProt C4R1V1 · UniProt C4R9A1 · UniProt C4R273 · UniProt F2QPE6 · UniProt C4R009 · UniProt C4R3Z5 · UniProt F2QMI1 · UniProt C4QZ45 · UniProt C4R0E6 · UniProt C4R370 · UniProt P84243 · UniProt P62805 · UniProt P04908 · UniProt P06899
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