6GYL
Structure of a yeast closed complex with distorted DNA (core CCdist)
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 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) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220 |
| 2 | B | DNA-directed RNA polymerase II subunit RPB2 | polymer | 1224 | 138937.3 | 1 | UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide |
| 3 | C | DNA-directed RNA polymerase II subunit RPB3 | polymer | 318 | 35330.5 | 1 | UniProt (P16370) Pfam (PF01193) Pfam (PF01000) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide |
| 4 | D | DNA-directed RNA polymerase II subunit RPB4 | polymer | 221 | 25451.2 | 1 | UniProt (P20433) Pfam (PF03874) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide |
| 5 | E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | polymer | 215 | 25117.1 | 1 | UniProt (P20434) Pfam (PF03871) Pfam (PF01191) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide |
| 6 | F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | polymer | 155 | 17931.8 | 1 | UniProt (P20435) Pfam (PF01192) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide |
| 7 | G | DNA-directed RNA polymerase II subunit RPB7 | polymer | 171 | 19081.1 | 1 | UniProt (P34087) Pfam (PF03876) Pfam (PF00575) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit B7,B16 |
| 8 | H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 146 | 16525.4 | 1 | UniProt (P20436) Pfam (PF03870) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / 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 |
| 9 | I | DNA-directed RNA polymerase II subunit RPB9 | polymer | 122 | 14308.2 | 1 | UniProt (P27999) Pfam (PF02150) Pfam (PF01096) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / 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 |
| 10 | J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 70 | 8290.7 | 1 | UniProt (P22139) Pfam (PF01194) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / 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 |
| 11 | K | DNA-directed RNA polymerase II subunit RPB11 | polymer | 120 | 13633.5 | 1 | UniProt (P38902) Pfam (PF13656) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide |
| 12 | L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | polymer | 70 | 7730.0 | 1 | UniProt (P40422) Pfam (PF03604) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA polymerases I,II,and III subunit ABC4,ABC10-alpha |
| 13 | M | Transcription initiation factor IIB | polymer | 345 | 38257.3 | 1 | UniProt (P29055) Pfam (PF08271) Pfam (PF00382) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | General transcription factor TFIIB,Transcription factor E |
| 14 | N | GAT1 promoter DNA | polymer | 56 | 17129.9 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | ||
| 15 | O | TATA-box-binding protein | polymer | 240 | 27042.3 | 1 | UniProt (P13393) Pfam (PF00352) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | TATA sequence-binding protein,TBP,TATA-binding factor,TATA-box factor,Transcription factor D,Transcription initiation factor TFIID TBP subunit |
| 16 | Q | Transcription initiation factor IIF subunit alpha | polymer | 735 | 82320.6 | 1 | UniProt (P41895) Pfam (PF05793) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | TFIIF-alpha,TFIIF large subunit,Transcription factor G 105 kDa subunit,P105 |
| 17 | R | Transcription initiation factor IIF subunit beta | polymer | 400 | 46684.5 | 1 | UniProt (P41896) Pfam (PF17683) Pfam (PF02270) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ATP-dependent helicase TFG2,TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit |
| 18 | T | GAT1 promoter DNA | polymer | 56 | 17388.1 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | ||
| 19 | U | Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit | polymer | 171 | 19432.0 | 1 | UniProt (P32773) Pfam (PF03153) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | TFIIA large subunit,TFIIA 32 kDa subunit,TFIIA large subunit,TFIIA 32 kDa subunit |
| 20 | V | Transcription initiation factor IIA subunit 2 | polymer | 129 | 14431.1 | 1 | UniProt (P32774) Pfam (PF02268) Pfam (PF02751) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | General transcription factor IIA subunit 2,TFIIA 13.5 kDa subunit,Transcription initiation factor IIA small chain,Transcription initiation factor IIA small subunit |
| 21 | W | Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1 | polymer | 586 | 57538.5 | 1 | UniProt (P36100) Pfam (PF02002) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit |
| 22 | X | Transcription initiation factor IIE subunit beta | polymer | 328 | 37050.4 | 1 | UniProt (P36145) Pfam (PF02186) Pfam (PF18121) Pfam (PF22254) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit |
| 23 | C, I, J, L, M... | ZINC ION | non-polymer | 65.4 | 10 | Chemie (ZN) | |||
| 24 | A | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
U: 1 - 209 (UniProt: P32773)
U: 210 - 286 (UniProt: P32773)
V: 1 - 122 (UniProt: P32774)
W: 1 - 194 (UniProt: P36100)
W: 195 - 513 (PDB: 6GYL)
W: 514 - 586 (PDB: 6GYL)
U: 210 - 286 (UniProt: P32773)
V: 1 - 122 (UniProt: P32774)
| PDB | External Database | Details |
|---|---|---|
| Lys 123 | - | expression tag |
| His 124 | - | expression tag |
| His 125 | - | expression tag |
| His 126 | - | expression tag |
| His 127 | - | expression tag |
| His 128 | - | expression tag |
| His 129 | - | expression tag |
W: 195 - 513 (PDB: 6GYL)
W: 514 - 586 (PDB: 6GYL)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 22 |
| Total formula weight | 871433.0 | |
| Non-Polymers* | Number of molecules | 11 |
| Total formula weight | 678.4 | |
| All* | Total formula weight | 872111.4 |
