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 (A) | DNA-directed RNA polymerase subunit | polymer | 1984 | 219049.5 | 1 | UniProt (A0A480RVL6) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) UniProt (by SIFTS) (A0A7M4DUC2) | Sus scrofa (Pig) | |
| 2 | B (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) | Sus scrofa (Pig) | |
| 3 | C (C) | RNA polymerase II subunit C | polymer | 275 | 31439.1 | 1 | UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) | Sus scrofa (Pig) | |
| 4 | D (D) | RNA polymerase II subunit D | polymer | 142 | 16331.3 | 1 | UniProt (A0A287ADR4) Pfam (PF03874) | Sus scrofa (Pig) | |
| 5 | E (E) | RNA polymerase II subunit E | polymer | 210 | 24644.3 | 1 | UniProt (I3LSI7) Pfam (PF03871) Pfam (PF01191) | Sus scrofa (Pig) | |
| 6 | F (F) | RNA polymerase II subunit F | polymer | 127 | 14477.0 | 1 | UniProt (F1SKN8) Pfam (PF01192) UniProt (by SIFTS) (A0A4X1VEK9) | Sus scrofa (Pig) | |
| 7 | G (G) | RNA polymerase II subunit G | polymer | 172 | 19314.3 | 1 | UniProt (I3LJZ9) | Sus scrofa (Pig) | |
| 8 | H (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 150 | 17162.3 | 1 | UniProt (I3LCB2) Pfam (PF03870) | Sus scrofa (Pig) | |
| 9 | I (I) | DNA-directed RNA polymerase II subunit RPB9 | polymer | 125 | 14541.2 | 1 | UniProt (P60899) Pfam (PF02150) Pfam (PF01096) | 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 (J) | Uncharacterized protein | polymer | 67 | 7655.1 | 1 | UniProt (A0A287B432) Pfam (PF01194) UniProt (by SIFTS) (A0A4X1VYD0) | Sus scrofa (Pig) | |
| 11 | K (K) | Uncharacterized protein | polymer | 117 | 13310.3 | 1 | UniProt (F1RKE4) Pfam (PF13656) | Sus scrofa (Pig) | |
| 12 | L (L) | Uncharacterized protein | polymer | 58 | 7018.2 | 1 | UniProt (I3LN51) Pfam (PF03604) UniProt (by SIFTS) (A0A4X1TRS6) | Sus scrofa (Pig) | |
| 13 | M (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) | Homo sapiens (Human) | hSPT6,Histone chaperone suppressor of Ty6,Tat-cotransactivator 2 protein,Tat-CT2 protein |
| 14 | N (N) | DNA (37-MER) | polymer | 48 | 14932.5 | 1 | synthetic construct | ||
| 15 | O (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 | P (Q) | RNA polymerase-associated protein CTR9 homolog | polymer | 1179 | 134510.2 | 1 | UniProt (Q6PD62) Pfam (PF13374) Pfam (PF13181) | Homo sapiens (Human) | SH2 domain-binding protein 1 |
| 17 | Q (R) | RNA polymerase-associated protein RTF1 homolog | polymer | 713 | 80733.0 | 1 | UniProt (Q92541) Pfam (PF03126) | Homo sapiens (Human) | |
| 18 | R (T) | Template DNA | polymer | 48 | 14672.3 | 1 | synthetic construct | ||
| 19 | S (U) | RNA polymerase-associated protein LEO1 | polymer | 666 | 75514.2 | 1 | UniProt (Q8WVC0) Pfam (PF04004) | Homo sapiens (Human) | Replicative senescence down-regulated leo1-like protein |
| 20 | T (V) | RNA polymerase II-associated factor 1 homolog | polymer | 531 | 60052.7 | 1 | UniProt (Q8N7H5) Pfam (PF03985) | Homo sapiens (Human) | hPAF1,Pancreatic differentiation protein 2 |
| 21 | U (W) | WD repeat-containing protein 61 | polymer | 305 | 33617.5 | 1 | UniProt (Q9GZS3) Pfam (PF00400) | Homo sapiens (Human) | Meiotic recombination REC14 protein homolog,SKI8 homolog,Ski8 |
| 22 | V (X) | Parafibromin | polymer | 531 | 60673.5 | 1 | UniProt (Q6P1J9) Pfam (PF16050) Pfam (PF05179) | Homo sapiens (Human) | Cell division cycle protein 73 homolog,Hyperparathyroidism 2 protein |
| 23 | W (Y) | Transcription elongation factor SPT4 | polymer | 121 | 13508.5 | 1 | UniProt (P63272) Pfam (PF06093) | Homo sapiens (Human) | hSPT4,DRB sensitivity-inducing factor 14 kDa subunit,DSIF p14,DRB sensitivity-inducing factor small subunit,DSIF small subunit |
| 24 | X (Z) | Transcription elongation factor SPT5 | polymer | 1087 | 121225.5 | 1 | UniProt (O00267) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) | 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 | BA, CA, DA, EA, FA... (B, C, I, J, L...) | ZINC ION | non-polymer | 65.4 | 9 | Chemie (ZN) | |||
| 26 | AA (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 |
