6TED
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A | DNA-directed RNA polymerase subunit | polymer | 1984 | 219049.5 | 1 | UniProt (A0A480RVL6) In PDB | Sus scrofa (Pig) | |
| 2 | B | DNA-directed RNA polymerase subunit beta | polymer | 1251 | 142426.1 | 1 | UniProt (I3LGP4) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB | Sus scrofa (Pig) | |
| 3 | C | RNA polymerase II subunit C | polymer | 275 | 31439.1 | 1 | UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) In PDB | Sus scrofa (Pig) | |
| 4 | D | RNA polymerase II subunit D | polymer | 142 | 16331.3 | 1 | UniProt (A0A287ADR4) Pfam (PF03874) In PDB | Sus scrofa (Pig) | |
| 5 | E | RNA polymerase II subunit E | polymer | 210 | 24644.3 | 1 | UniProt (I3LSI7) Pfam (PF03871) Pfam (PF01191) In PDB | Sus scrofa (Pig) | |
| 6 | F | RNA polymerase II subunit F | polymer | 127 | 14477.0 | 1 | UniProt (F1SKN8) Pfam (PF01192) UniProt (by SIFTS) (A0A4X1VEK9) In PDB | Sus scrofa (Pig) | |
| 7 | G | RNA polymerase II subunit G | polymer | 172 | 19314.3 | 1 | UniProt (I3LJZ9) In PDB | Sus scrofa (Pig) | |
| 8 | H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 150 | 17162.3 | 1 | UniProt (I3LCB2) Pfam (PF03870) In PDB | Sus scrofa (Pig) | |
| 9 | I | DNA-directed RNA polymerase II subunit RPB9 | polymer | 125 | 14541.2 | 1 | UniProt (P60899) Pfam (PF02150) Pfam (PF01096) In PDB | Sus scrofa (Pig) | RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5 |
| 10 | J | Uncharacterized protein | polymer | 67 | 7655.1 | 1 | UniProt (A0A287B432) Pfam (PF01194) UniProt (by SIFTS) (A0A4X1VYD0) In PDB | Sus scrofa (Pig) | |
| 11 | K | Uncharacterized protein | polymer | 117 | 13310.3 | 1 | UniProt (F1RKE4) Pfam (PF13656) In PDB | Sus scrofa (Pig) | |
| 12 | L | Uncharacterized protein | polymer | 58 | 7018.2 | 1 | UniProt (I3LN51) Pfam (PF03604) UniProt (by SIFTS) (A0A4X1TRS6) In PDB | Sus scrofa (Pig) | |
| 13 | M | Transcription elongation factor SPT6 | polymer | 1729 | 199603.0 | 1 | UniProt (Q7KZ85) Pfam (PF14632) Pfam (PF14641) Pfam (PF22706) Pfam (PF14639) Pfam (PF14635) Pfam (PF17674) Pfam (PF00575) Pfam (PF14633) In PDB | Homo sapiens (Human) | hSPT6,Histone chaperone suppressor of Ty6,Tat-cotransactivator 2 protein,Tat-CT2 protein |
| 14 | N | DNA (37-MER) | polymer | 48 | 14932.5 | 1 | synthetic construct | ||
| 15 | P | RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') | polymer | 46 | 14843.9 | 1 | synthetic construct | ||
| 16 | Q | RNA polymerase-associated protein CTR9 homolog | polymer | 1179 | 134510.2 | 1 | UniProt (Q6PD62) Pfam (PF13374) Pfam (PF13181) In PDB | Homo sapiens (Human) | SH2 domain-binding protein 1 |
| 17 | R | RNA polymerase-associated protein RTF1 homolog | polymer | 713 | 80733.0 | 1 | UniProt (Q92541) Pfam (PF03126) In PDB | Homo sapiens (Human) | |
| 18 | T | Template DNA | polymer | 48 | 14672.3 | 1 | synthetic construct | ||
| 19 | U | RNA polymerase-associated protein LEO1 | polymer | 666 | 75514.2 | 1 | UniProt (Q8WVC0) Pfam (PF04004) In PDB | Homo sapiens (Human) | Replicative senescence down-regulated leo1-like protein |
| 20 | V | RNA polymerase II-associated factor 1 homolog | polymer | 531 | 60052.7 | 1 | UniProt (Q8N7H5) Pfam (PF03985) In PDB | Homo sapiens (Human) | hPAF1,Pancreatic differentiation protein 2 |
| 21 | W | WD repeat-containing protein 61 | polymer | 305 | 33617.5 | 1 | UniProt (Q9GZS3) Pfam (PF00400) In PDB | Homo sapiens (Human) | Meiotic recombination REC14 protein homolog,SKI8 homolog,Ski8 |
| 22 | X | Parafibromin | polymer | 531 | 60673.5 | 1 | UniProt (Q6P1J9) Pfam (PF16050) Pfam (PF05179) In PDB | Homo sapiens (Human) | Cell division cycle protein 73 homolog,Hyperparathyroidism 2 protein |
| 23 | Y | Transcription elongation factor SPT4 | polymer | 121 | 13508.5 | 1 | UniProt (P63272) Pfam (PF06093) In PDB | Homo sapiens (Human) | hSPT4,DRB sensitivity-inducing factor 14 kDa subunit,DSIF p14,DRB sensitivity-inducing factor small subunit,DSIF small subunit |
| 24 | Z | Transcription elongation factor SPT5 | polymer | 1087 | 121225.5 | 1 | UniProt (O00267) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) In PDB | Homo sapiens (Human) | hSPT5,DRB sensitivity-inducing factor 160 kDa subunit,DSIF p160,DRB sensitivity-inducing factor large subunit,DSIF large subunit,Tat-cotransactivator 1 protein,Tat-CT1 protein |
| 25 | B, C, I, J, L... | ZINC ION | non-polymer | 65.4 | 9 | Chemie (ZN) | |||
| 26 | A | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
M: 1 - 1726 (UniProt: Q7KZ85)
Q: 1 - 1173 (UniProt: Q6PD62)
R: 1 - 710 (UniProt: Q92541)
Y: 1 - 117 (UniProt: P63272)
| PDB | External Database | Details |
|---|---|---|
| Ser -2 | - | expression tag |
| Asn -1 | - | expression tag |
| Ala 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Glu 1174 | - | expression tag |
| Asn 1175 | - | expression tag |
| Leu 1176 | - | expression tag |
| Tyr 1177 | - | expression tag |
| Phe 1178 | - | expression tag |
| Gln 1179 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Ser -2 | - | expression tag |
| Asn -1 | - | expression tag |
| Ala 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -3 | - | expression tag |
| Pro -2 | - | expression tag |
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 1351255.5 | |
| Non-Polymers* | Number of molecules | 10 |
| Total formula weight | 613.0 | |
| All* | Total formula weight | 1351868.5 |
