8YFQ
Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex
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 | 1743 | 194107.4 | 1 | UniProt (C4R4Y0) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) | Komagataella phaffii | RNA polymerase II subunit Rpb1 |
| 2 | B (B) | DNA-directed RNA polymerase subunit beta | polymer | 1227 | 139746.1 | 1 | UniProt (C4QZQ7) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) | Komagataella phaffii | RNA polymerase II subunit Rpb2 |
| 3 | C (C) | RNA polymerase II third largest subunit B44, part of central core | polymer | 304 | 34216.3 | 1 | UniProt (C4R7L2) Pfam (PF01193) Pfam (PF01000) | Komagataella phaffii | RNA polymerase II subunit Rpb3 |
| 4 | D (D) | RNA polymerase II subunit B32 | polymer | 186 | 20623.0 | 1 | UniProt (C4R2U9) Pfam (PF03874) | Komagataella phaffii | RNA polymerase II subunit Rpb4 |
| 5 | E (E) | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | polymer | 214 | 24962.7 | 1 | UniProt (C4R3P8) Pfam (PF03871) Pfam (PF01191) | Komagataella phaffii | RNA polymerase II subunit Rpb5 |
| 6 | F (F) | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | polymer | 155 | 17803.6 | 1 | UniProt (C4R1V1) Pfam (PF01192) | Komagataella phaffii | RNA polymerase II subunit Rpb6 |
| 7 | G (G) | RNA polymerase II subunit | polymer | 171 | 18802.6 | 1 | UniProt (C4R9A1) Pfam (PF03876) Pfam (PF00575) | Komagataella phaffii | RNA polymerase II subunit Rpb7 |
| 8 | H (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 145 | 16249.2 | 1 | UniProt (C4R273) Pfam (PF03870) | Komagataella phaffii | RNA polymerase II subunit Rpb8 |
| 9 | I (I) | DNA-directed RNA polymerase subunit | polymer | 115 | 13612.3 | 1 | UniProt (F2QPE6) Pfam (PF02150) Pfam (PF01096) UniProt (by SIFTS) (C4QY79) | Komagataella phaffii | |
| 10 | J (J) | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | polymer | 72 | 8554.1 | 1 | UniProt (C4R009) Pfam (PF01194) | Komagataella phaffii | RNA polymerase II subunit Rpb10 |
| 11 | K (K) | RNA polymerase II subunit B12.5 | polymer | 118 | 13832.9 | 1 | UniProt (C4R3Z5) Pfam (PF13656) | Komagataella phaffii | RNA polymerase II subunit Rpb11 |
| 12 | L (L) | RNA polymerase subunit ABC10-alpha | polymer | 72 | 7862.0 | 1 | UniProt (F2QMI1) Pfam (PF03604) UniProt (by SIFTS) (C4QWA8) | Komagataella phaffii | RNA polymerase II subunit Rpb12 |
| 13 | M (N) | DNA (90-mer) | polymer | 90 | 27700.8 | 1 | synthetic construct | ||
| 14 | N (T) | DNA (90-mer) | polymer | 90 | 27788.8 | 1 | synthetic construct | ||
| 15 | O (P) | RNA (22-mer) | polymer | 22 | 7050.3 | 1 | synthetic construct | ||
| 16 | P (R) | 5'-3' exoribonuclease | polymer | 1006 | 115397.6 | 1 | UniProt (F2QV79) Pfam (PF03159) Pfam (PF17846) UniProt (by SIFTS) (C4R5R1) | Komagataella phaffii | |
| 17 | Q (S) | Decapping nuclease | polymer | 384 | 44596.0 | 1 | UniProt (F2QLF5) Pfam (PF08652) UniProt (by SIFTS) (C4QXY9) | Komagataella phaffii | |
| 18 | R, S, U, V, W... (A, B, C, I, J...) | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) | |||
| 19 | T (A) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
R: 1 - 994 (UniProt: F2QV79)
S: 1 - 381 (UniProt: F2QLF5)
| PDB | External Database | Details |
|---|---|---|
| Gln 203 | Glu 203 | engineered mutation |
| Gln 205 | Glu 205 | engineered mutation |
| Asn 233 | Asp 233 | engineered mutation |
| Asn 235 | Asp 235 | engineered mutation |
| Asn 330 | Asp 330 | engineered mutation |
| Ser 995 | - | expression tag |
| Gly 996 | - | expression tag |
| Pro 997 | - | expression tag |
| Ser 998 | - | expression tag |
| Ser 999 | - | expression tag |
| Gly 1000 | - | expression tag |
| Leu 1001 | - | expression tag |
| Glu 1002 | - | expression tag |
| Val 1003 | - | expression tag |
| Leu 1004 | - | expression tag |
| Phe 1005 | - | expression tag |
| Gln 1006 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Pro -1 | - | expression tag |
| Gly 0 | - | expression tag |
| Ala 213 | Glu 213 | engineered mutation |
| Ala 215 | Asp 215 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 17 |
| Total formula weight | 732905.6 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 547.6 | |
| All* | Total formula weight | 733453.2 |
