5XOG
RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1
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 | 1743 | 194107.4 | 1 | UniProt (C4R4Y0) Pfam (PF04997) Pfam (PF05001) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb1 |
| 2 | 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) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb2 |
| 3 | C | RNA polymerase II third largest subunit B44, part of central core | polymer | 304 | 34216.3 | 1 | UniProt (C4R7L2) Pfam (PF01193) Pfam (PF01000) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb3 |
| 4 | D | RNA polymerase II subunit B32 | polymer | 186 | 20623.0 | 1 | UniProt (C4R2U9) Pfam (PF03874) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb4 |
| 5 | E | RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III | polymer | 214 | 24962.7 | 1 | UniProt (C4R3P8) Pfam (PF03871) Pfam (PF01191) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb5 |
| 6 | F | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | polymer | 155 | 17803.6 | 1 | UniProt (C4R1V1) Pfam (PF01192) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb6 |
| 7 | G | RNA polymerase II subunit | polymer | 171 | 18802.6 | 1 | UniProt (C4R9A1) Pfam (PF03876) Pfam (PF00575) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb7 |
| 8 | H | RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III | polymer | 145 | 16249.2 | 1 | UniProt (C4R273) Pfam (PF03870) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb8 |
| 9 | I | DNA-directed RNA polymerase subunit | polymer | 115 | 13612.3 | 1 | UniProt (F2QPE6) Pfam (PF02150) Pfam (PF01096) In PDB | Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (Yeast) | RNA polymerase II subunit Rpb9 |
| 10 | J | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | polymer | 72 | 8554.1 | 1 | UniProt (C4R009) Pfam (PF01194) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb10 |
| 11 | K | RNA polymerase II subunit B12.5 | polymer | 118 | 13832.9 | 1 | UniProt (C4R3Z5) Pfam (PF13656) In PDB | Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) | RNA polymerase II subunit Rpb11 |
| 12 | L | RNA polymerase subunit ABC10-alpha | polymer | 72 | 7862.0 | 1 | UniProt (F2QMI1) Pfam (PF03604) In PDB | Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (Yeast) | RNA polymerase II subunit Rpb12 |
| 13 | P | RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') | polymer | 17 | 5384.2 | 1 | synthetic construct | ||
| 14 | T | DNA (39-MER) | polymer | 39 | 11909.7 | 1 | synthetic construct | ||
| 15 | N | DNA (30-MER) | polymer | 30 | 9316.0 | 1 | synthetic construct | ||
| 16 | M | Transcription elongation factor 1 homolog | polymer | 85 | 9414.9 | 1 | UniProt (A0A1B2JER8) Pfam (PF05129) In PDB | Komagataella pastoris (Yeast) | Transcription elongation factor Elf1 |
| 17 | W | Spt4/5 complex component | polymer | 83 | 9201.5 | 1 | UniProt (F2QUC3) Pfam (PF00467) In PDB | Komagataella phaffii (Yeast) | Transcription elongation factor Spt5 |
| 18 | L, M, A, B, C... | ZINC ION | non-polymer | 65.4 | 9 | Chemie (ZN) | |||
| 19 | A | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 20 | A | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER | non-polymer | 505.2 | 1 | Chemie (APC) |
Sequence modifications
M: 1 - 82 (UniProt: A0A1B2JER8)
W: 736 - 815 (UniProt: F2QUC3)
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Pro -1 | - | expression tag |
| Gly 0 | - | expression tag |
| Gly 53 | Asn 53 | engineered mutation |
| Gln 54 | Leu 54 | engineered mutation |
| Arg 55 | Ser 55 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly 733 | - | expression tag |
| Pro 734 | - | expression tag |
| Gly 735 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 17 |
| Total formula weight | 555598.4 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 1118.2 | |
| All* | Total formula weight | 556716.6 |
