8K5P
Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2)
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 II subunit RPB1 | polymer | 1733 | 191821.6 | 1 | UniProt (P04050) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit 1,RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220 |
| 2 | B (B) | DNA-directed RNA polymerase II subunit RPB2 | polymer | 1259 | 143336.8 | 1 | UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide |
| 3 | C (C) | DNA-directed RNA polymerase II subunit RPB3 | polymer | 318 | 35330.5 | 1 | UniProt (P16370) Pfam (PF01193) Pfam (PF01000) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit 3,RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide |
| 4 | D (E) | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | polymer | 215 | 25117.1 | 1 | UniProt (P20434) Pfam (PF03871) Pfam (PF01191) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide |
| 5 | E (F) | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | polymer | 155 | 17931.8 | 1 | UniProt (P20435) Pfam (PF01192) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide |
| 6 | F (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 146 | 16525.4 | 1 | UniProt (P20436) Pfam (PF03870) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide |
| 7 | G (I) | DNA-directed RNA polymerase II subunit RPB9 | polymer | 122 | 14308.2 | 1 | UniProt (P27999) Pfam (PF02150) Pfam (PF01096) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9 |
| 8 | H (J) | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 70 | 8290.7 | 1 | UniProt (P22139) Pfam (PF01194) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide |
| 9 | I (K) | DNA-directed RNA polymerase II subunit RPB11 | polymer | 120 | 13633.5 | 1 | UniProt (P38902) Pfam (PF13656) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide |
| 10 | J (L) | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | polymer | 70 | 7730.0 | 1 | UniProt (P40422) Pfam (PF03604) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerases I,II,and III subunit ABC4,ABC10-alpha |
| 11 | K (N) | DNA (38-MER) | polymer | 48 | 14935.6 | 1 | synthetic construct | ||
| 12 | L (P) | RNA | polymer | 20 | 6446.9 | 1 | synthetic construct | ||
| 13 | M (T) | DNA (38-MER) | polymer | 48 | 14633.4 | 1 | synthetic construct | ||
| 14 | N (W) | Transcription elongation factor SPT5 | polymer | 1070 | 116758.0 | 1 | UniProt (P27692) Pfam (PF11942) Pfam (PF03439) Pfam (PF00467) Pfam (PF12815) | Saccharomyces cerevisiae S288C (baker's yeast) | Chromatin elongation factor SPT5 |
| 15 | O (D) | DNA-directed RNA polymerase II subunit RPB4 | polymer | 221 | 25451.2 | 1 | UniProt (P20433) Pfam (PF03874) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide |
| 16 | P (G) | DNA-directed RNA polymerase II subunit RPB7 | polymer | 171 | 19081.1 | 1 | UniProt (P34087) Pfam (PF03876) Pfam (PF00575) | Saccharomyces cerevisiae S288C (baker's yeast) | RNA polymerase II subunit B7,B16 |
| 17 | Q (M) | 5'-3' exoribonuclease 2 | polymer | 1019 | 117606.5 | 1 | UniProt (Q02792) Pfam (PF03159) Pfam (PF17846) | Saccharomyces cerevisiae S288C (baker's yeast) | Ribonucleic acid-trafficking protein 1,p116 |
| 18 | R (O) | Decapping nuclease RAI1 | polymer | 387 | 44571.4 | 1 | UniProt (P53063) Pfam (PF08652) | Saccharomyces cerevisiae S288C (baker's yeast) | ScRai1,NAD-capped RNA hydrolase RAI1,DeNADding enzyme RAI1,RAT1-interacting protein |
| 19 | AA, S, T, V, W... (L, A, B, C, I...) | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) | |||
| 20 | BA, CA, U (M, O, A) | MAGNESIUM ION | non-polymer | 24.3 | 3 | Chemie (MG) |
Sequence modifications
B: 1 - 1224 (UniProt: P08518)
W: 1 - 1063 (UniProt: P27692)
M: 1 - 1006 (UniProt: Q02792)
| PDB | External Database | Details |
|---|---|---|
| Glu 1225 | - | expression tag |
| Asn 1226 | - | expression tag |
| Leu 1227 | - | expression tag |
| Tyr 1228 | - | expression tag |
| Phe 1229 | - | expression tag |
| Gln 1230 | - | expression tag |
| Gly 1231 | - | expression tag |
| His 1232 | - | expression tag |
| His 1233 | - | expression tag |
| His 1234 | - | expression tag |
| His 1235 | - | expression tag |
| His 1236 | - | expression tag |
| His 1237 | - | expression tag |
| Asp 1238 | - | expression tag |
| Tyr 1239 | - | expression tag |
| Lys 1240 | - | expression tag |
| Asp 1241 | - | expression tag |
| His 1242 | - | expression tag |
| Asp 1243 | - | expression tag |
| Gly 1244 | - | expression tag |
| Asp 1245 | - | expression tag |
| Tyr 1246 | - | expression tag |
| Lys 1247 | - | expression tag |
| Asp 1248 | - | expression tag |
| His 1249 | - | expression tag |
| Asp 1250 | - | expression tag |
| Ile 1251 | - | expression tag |
| Asp 1252 | - | expression tag |
| Tyr 1253 | - | expression tag |
| Lys 1254 | - | expression tag |
| Asp 1255 | - | expression tag |
| Asp 1256 | - | expression tag |
| Asp 1257 | - | expression tag |
| Asp 1258 | - | expression tag |
| Lys 1259 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met -6 | - | initiating methionine |
| His -5 | - | expression tag |
| His -4 | - | expression tag |
| His -3 | - | expression tag |
| His -2 | - | expression tag |
| His -1 | - | expression tag |
| His 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met -12 | - | initiating methionine |
| Gly -11 | - | expression tag |
| Ser -10 | - | expression tag |
| Ser -9 | - | expression tag |
| His -8 | - | expression tag |
| His -7 | - | expression tag |
| His -6 | - | expression tag |
| His -5 | - | expression tag |
| His -4 | - | expression tag |
| His -3 | - | expression tag |
| Ser -2 | - | expression tag |
| Gln -1 | - | expression tag |
| Asp 0 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 18 |
| Total formula weight | 833509.6 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 596.2 | |
| All* | Total formula weight | 834105.7 |
