5SVA
Mediator-RNA Polymerase II Pre-Initiation Complex
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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (Baker's yeast) | RNA polymerases I, II, and III subunit ABC4, ABC10-alpha |
| 13 | M | Mediator of RNA polymerase II transcription subunit 6 | polymer | 295 | 32844.7 | 1 | UniProt (P38782) Pfam (PF04934) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 6 |
| 14 | N | Mediator of RNA polymerase II transcription subunit 8 | polymer | 223 | 25297.2 | 1 | UniProt (P38304) Pfam (PF10232) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 8 |
| 15 | O | Mediator of RNA polymerase II transcription subunit 11 | polymer | 115 | 13324.2 | 1 | UniProt (Q99278) Pfam (PF10280) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 11 |
| 16 | P | Mediator of RNA polymerase II transcription subunit 17 | polymer | 687 | 78582.8 | 1 | UniProt (P32569) Pfam (PF10156) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 17, Suppressor of RNA polymerase B 4 |
| 17 | Q | Mediator of RNA polymerase II transcription subunit 18 | polymer | 307 | 34316.5 | 1 | UniProt (P32585) Pfam (PF09637) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 18, Suppressor of RNA polymerase B 5 |
| 18 | R | Mediator of RNA polymerase II transcription subunit 20 | polymer | 210 | 22918.1 | 1 | UniProt (P34162) Pfam (PF08612) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Hyper-recombination suppressor protein 2, Mediator complex subunit 20, Suppressor of RNA polymerase B 2 |
| 19 | S | Mediator of RNA polymerase II transcription subunit 22 | polymer | 121 | 13875.7 | 1 | UniProt (P32570) Pfam (PF06179) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 22, Suppressor of RNA polymerase B 6 |
| 20 | T | Mediator of RNA polymerase II transcription subunit 4 | polymer | 284 | 32244.9 | 1 | UniProt (Q12343) Pfam (PF10018) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 4 |
| 21 | U | Mediator of RNA polymerase II transcription subunit 7 | polymer | 222 | 25616.1 | 1 | UniProt (Q08278) Pfam (PF05983) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 7 |
| 22 | V | Mediator of RNA polymerase II transcription subunit 9 | polymer | 149 | 17400.4 | 1 | UniProt (P33308) Pfam (PF07544) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Chromosome segregation protein 2, Mediator complex subunit 9 |
| 23 | W | Mediator of RNA polymerase II transcription subunit 21 | polymer | 140 | 16093.4 | 1 | UniProt (P47822) Pfam (PF11221) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Mediator complex subunit 21, RNAPII complex component SRB7, Suppressor of RNA polymerase B 7 |
| 24 | X | Mediator of RNA polymerase II transcription subunit 31 | polymer | 127 | 14747.7 | 1 | UniProt (P38633) Pfam (PF05669) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Hpr1 suppressor protein 1, Mediator complex subunit 31 |
| 25 | Y | DNA repair helicase RAD3 | polymer | 778 | 89899.0 | 1 | UniProt (P06839) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) In PDB | Saccharomyces cerevisiae (Baker's yeast) | General transcription and DNA repair factor IIH subunit RAD3, TFIIH subunit RAD3 |
| 26 | Z | DNA repair helicase RAD25 | polymer | 843 | 95461.7 | 1 | UniProt (Q00578) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) In PDB | Saccharomyces cerevisiae (Baker's yeast) | General transcription and DNA repair factor IIH subunit RAD25, TFIIH subunit RAD25, Suppressor of stem-loop mutation 2 |
| 27 | a | RNA polymerase II transcription factor B subunit 2 | polymer | 513 | 58602.3 | 1 | UniProt (Q02939) Pfam (PF03849) Pfam (PF18307) In PDB | Saccharomyces cerevisiae (Baker's yeast) | General transcription and DNA repair factor IIH subunit TFB2, TFIIH subunit TFB2, RNA polymerase II transcription factor B 52 kDa subunit, RNA polymerase II transcription factor B p52 subunit |
| 28 | b | RNA polymerase II transcription factor B subunit 5 | polymer | 72 | 8243.5 | 1 | UniProt (Q3E7C1) Pfam (PF06331) In PDB | Saccharomyces cerevisiae (Baker's yeast) | General transcription and DNA repair factor IIH subunit TFB5, TFIIH subunit TFB5 |
| 29 | c | Transcription initiation factor IIB | polymer | 345 | 38257.3 | 1 | UniProt (P29055) Pfam (PF08271) Pfam (PF00382) In PDB | Saccharomyces cerevisiae (Baker's yeast) | General transcription factor TFIIB, Transcription factor E |
| 30 | d | Transcription initiation factor IIA large subunit | polymer | 286 | 32230.8 | 1 | UniProt (P32773) Pfam (PF03153) In PDB | Saccharomyces cerevisiae (Baker's yeast) | TFIIA large subunit, TFIIA 32 kDa subunit |
| 31 | e | Transcription initiation factor IIA subunit 2 | polymer | 122 | 13473.1 | 1 | UniProt (P32774) Pfam (PF02268) Pfam (PF02751) In PDB | Saccharomyces cerevisiae (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 |
| 32 | f | Transcription initiation factor IIF subunit alpha | polymer | 735 | 82320.6 | 1 | UniProt (P41895) Pfam (PF05793) In PDB | Saccharomyces cerevisiae (Baker's yeast) | TFIIF-alpha, TFIIF large subunit, Transcription factor G 105 kDa subunit, P105 |
| 33 | g | Transcription initiation factor IIF subunit beta | polymer | 400 | 46684.5 | 1 | UniProt (P41896) Pfam (PF17683) Pfam (PF02270) In PDB | Saccharomyces cerevisiae (Baker's yeast) | ATP-dependent helicase TFG2, TFIIF medium subunit, TFIIF-beta, Transcription factor G 54 kDa subunit |
| 34 | h | Transcription initiation factor IIE subunit alpha | polymer | 482 | 54804.8 | 1 | UniProt (P36100) Pfam (PF02002) In PDB | Saccharomyces cerevisiae (Baker's yeast) | TFIIE-alpha, Factor A 66 kDa subunit, Transcription factor A large subunit |
| 35 | i | Transcription initiation factor IIE subunit beta | polymer | 328 | 37050.4 | 1 | UniProt (P36145) Pfam (PF02186) Pfam (PF18121) Pfam (PF22254) In PDB | Saccharomyces cerevisiae (Baker's yeast) | TFIIE-beta, Factor A 43 kDa subunit, Transcription factor A small subunit |
| 36 | j | TATA-box-binding protein | polymer | 240 | 27042.3 | 1 | UniProt (P13393) Pfam (PF00352) In PDB | Saccharomyces cerevisiae (Baker's yeast) | TATA sequence-binding protein, TBP, TATA-binding factor, TATA-box factor, Transcription factor D, Transcription initiation factor TFIID TBP subunit |
| 37 | k | DNA-directed RNA polymerase II subunit RPB1 | polymer | 25 | 2611.7 | 1 | UniProt (P04050) Pfam (PF05001) In PDB | Saccharomyces cerevisiae | RNA polymerase II subunit B1, DNA-directed RNA polymerase III largest subunit, RNA polymerase II subunit B220 |
| 38 | l | 108bp HIS4 Promoter Non-template Strand (-92/+16) | polymer | 108 | 33323.4 | 1 | Saccharomyces cerevisiae | ||
| 39 | m | 108bp HIS4 Promoter Template Strand (+16/-92) | polymer | 108 | 33305.4 | 1 | Saccharomyces cerevisiae | ||
| 40 | n | Transcription initiation factor TFIID subunit 14 | polymer | 244 | 27473.2 | 1 | UniProt (P35189) Pfam (PF03366) Pfam (PF17035) In PDB | Saccharomyces cerevisiae (Baker's yeast) | Actin non-complementing mutant 1, Chromosome stability protein 10, SWI/SNF chromatin-remodeling complex subunit TAF14, SWI/SNF complex 29 kDa subunit, SWI/SNF complex subunit TAF14, TBP-associated factor 14, TBP-associated factor 30 kDa, Transcription factor G 30 kDa subunit, Transcription initiation factor TFIIF 30 kDa subunit |
| 41 | A, B, C, I, J... | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) | |||
| 42 | A | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 40 |
| Total formula weight | 1522203.9 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 547.6 | |
| All* | Total formula weight | 1522751.5 |
