7ZS9
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A)
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 (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) | Saccharomyces cerevisiae | 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 | 1224 | 138937.3 | 1 | UniProt (P08518) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) | Saccharomyces cerevisiae | 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 | 347 | 38635.9 | 1 | UniProt (P16370) Pfam (PF01193) Pfam (PF01000) | Saccharomyces cerevisiae | RNA polymerase II subunit 3,RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide |
| 4 | D (D) | DNA-directed RNA polymerase II subunit RPB4 | polymer | 221 | 25451.2 | 1 | UniProt (P20433) Pfam (PF03874) | Saccharomyces cerevisiae | RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide |
| 5 | E (E) | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | polymer | 215 | 25117.1 | 1 | UniProt (P20434) Pfam (PF03871) Pfam (PF01191) | Saccharomyces cerevisiae | RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide |
| 6 | F (F) | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | polymer | 155 | 17931.8 | 1 | UniProt (P20435) Pfam (PF01192) | Saccharomyces cerevisiae | RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide |
| 7 | G (G) | DNA-directed RNA polymerase II subunit RPB7 | polymer | 177 | 19909.9 | 1 | UniProt (P34087) Pfam (PF03876) Pfam (PF00575) | Saccharomyces cerevisiae | RNA polymerase II subunit B7,B16 |
| 8 | H (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 146 | 16525.4 | 1 | UniProt (P20436) Pfam (PF03870) | Saccharomyces cerevisiae | 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 (I) | DNA-directed RNA polymerase II subunit RPB9 | polymer | 122 | 14308.2 | 1 | UniProt (P27999) Pfam (PF02150) Pfam (PF01096) | Saccharomyces cerevisiae | 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 (J) | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 70 | 8290.7 | 1 | UniProt (P22139) Pfam (PF01194) | Saccharomyces cerevisiae | RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide |
| 11 | K (K) | DNA-directed RNA polymerase II subunit RPB11 | polymer | 120 | 13633.5 | 1 | UniProt (P38902) Pfam (PF13656) | Saccharomyces cerevisiae | RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide |
| 12 | L (L) | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | polymer | 70 | 7730.0 | 1 | UniProt (P40422) Pfam (PF03604) | Saccharomyces cerevisiae | RNA polymerases I,II,and III subunit ABC4,ABC10-alpha |
| 13 | M (M) | Transcription initiation factor IIB | polymer | 352 | 39215.4 | 1 | UniProt (P29055) Pfam (PF08271) Pfam (PF00382) | Saccharomyces cerevisiae (baker's yeast) | General transcription factor TFIIB,Transcription factor E |
| 14 | N (N) | Non-template DNA (209-MER) | polymer | 209 | 64291.0 | 1 | synthetic construct | ||
| 15 | O (O) | TATA-box-binding protein | polymer | 247 | 28000.3 | 1 | UniProt (P13393) Pfam (PF00352) | 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 |
| 16 | P (Q) | Transcription initiation factor IIF subunit alpha | polymer | 738 | 82531.8 | 1 | UniProt (P41895) Pfam (PF05793) | Saccharomyces cerevisiae (baker's yeast) | TFIIF-alpha,TFIIF large subunit,Transcription factor G 105 kDa subunit,P105 |
| 17 | Q (R) | Transcription initiation factor IIF subunit beta | polymer | 400 | 46684.5 | 1 | UniProt (P41896) Pfam (PF17683) Pfam (PF02270) | Saccharomyces cerevisiae (baker's yeast) | TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit |
| 18 | R (T) | Template DNA (209-MER) | polymer | 209 | 64754.3 | 1 | synthetic construct | ||
| 19 | S (U) | Transcription initiation factor IIA large subunit | polymer | 171 | 19432.0 | 1 | Pfam (PF03153) UniProt (by SIFTS) (P32773) | Saccharomyces cerevisiae | |
| 20 | T (V) | Transcription initiation factor IIA subunit 2 | polymer | 129 | 14431.1 | 1 | UniProt (P32774) Pfam (PF02268) Pfam (PF02751) | 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 |
| 21 | U (W) | Transcription initiation factor IIE subunit alpha | polymer | 492 | 55951.0 | 1 | UniProt (P36100) Pfam (PF02002) | Saccharomyces cerevisiae (baker's yeast) | TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit |
| 22 | V (X) | Transcription initiation factor IIE subunit beta | polymer | 328 | 37050.4 | 1 | UniProt (P36145) Pfam (PF02186) Pfam (PF18121) Pfam (PF22254) | Saccharomyces cerevisiae (baker's yeast) | TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit |
| 23 | W (0) | General transcription and DNA repair factor IIH helicase subunit XPD | polymer | 778 | 89899.0 | 1 | UniProt (P06839) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3 |
| 24 | X (1) | General transcription and DNA repair factor IIH subunit TFB1 | polymer | 645 | 73194.5 | 1 | UniProt (P32776) Pfam (PF08567) Pfam (PF03909) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1 |
| 25 | Y (2) | General transcription and DNA repair factor IIH subunit TFB2 | polymer | 517 | 58900.6 | 1 | UniProt (Q02939) Pfam (PF03849) Pfam (PF18307) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2 |
| 26 | Z (3) | RNA polymerase II transcription factor B subunit 3 | polymer | 324 | 38480.7 | 1 | UniProt (Q03290) Pfam (PF06391) Pfam (PF17121) | Saccharomyces cerevisiae (baker's yeast) | RNA polymerase II transcription factor B 38 kDa subunit,RNA polymerase II transcription factor B p38 subunit |
| 27 | AA (4) | General transcription and DNA repair factor IIH subunit TFB4 | polymer | 341 | 37778.7 | 1 | UniProt (Q12004) Pfam (PF03850) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4 |
| 28 | BA (5) | General transcription and DNA repair factor IIH subunit TFB5 | polymer | 76 | 8541.8 | 1 | UniProt (Q3E7C1) Pfam (PF06331) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit TFB5,RNA polymerase II transcription factor B subunit 5 |
| 29 | CA (6) | General transcription and DNA repair factor IIH subunit SSL1 | polymer | 464 | 52571.2 | 1 | UniProt (Q04673) Pfam (PF04056) Pfam (PF07975) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1 |
| 30 | DA (7) | General transcription and DNA repair factor IIH helicase subunit XPB | polymer | 843 | 95461.7 | 1 | UniProt (Q00578) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2 |
| 31 | EA, IA (a, e) | Histone H3.2 | polymer | 135 | 15271.9 | 2 | UniProt (P84233) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 32 | FA, JA (b, f) | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 33 | GA, KA (c, g) | Histone H2A | polymer | 129 | 13978.2 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) UniProt (by SIFTS) (P06897) | Xenopus laevis (African clawed frog) | |
| 34 | HA, LA (d, h) | Histone H2B 1.1 | polymer | 125 | 13848.1 | 2 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 35 | AB, BB, CB, DB, EB... (4, 6, A, B, C...) | ZINC ION | non-polymer | 65.4 | 17 | Chemie (ZN) | |||
| 36 | OA (A) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 37 | XA (0) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 1 | Chemie (SF4) |
Sequence modifications
C: 4 - 318 (UniProt: P16370)
G: 1 - 171 (UniProt: P34087)
M: 1 - 345 (UniProt: P29055)
O: 1 - 240 (UniProt: P13393)
Q: 1 - 735 (UniProt: P41895)
V: 1 - 122 (UniProt: P32774)
W: 1 - 482 (UniProt: P36100)
1: 1 - 642 (UniProt: P32776)
2: 1 - 513 (UniProt: Q02939)
3: 1 - 321 (UniProt: Q03290)
4: 1 - 338 (UniProt: Q12004)
5: 1 - 72 (UniProt: Q3E7C1)
6: 1 - 461 (UniProt: Q04673)
a, e: 1 - 135 (UniProt: P84233)
d, h: -2 - 122 (UniProt: P02281)
| PDB | External Database | Details |
|---|---|---|
| Met -28 | - | initiating methionine |
| Gly -27 | - | expression tag |
| Ser -26 | - | expression tag |
| His -25 | - | expression tag |
| His -24 | - | expression tag |
| His -23 | - | expression tag |
| His -22 | - | expression tag |
| His -21 | - | expression tag |
| His -20 | - | expression tag |
| Ser -19 | - | expression tag |
| Asn -18 | - | expression tag |
| Ser -17 | - | expression tag |
| Gly -16 | - | expression tag |
| Leu -15 | - | expression tag |
| Asn -14 | - | expression tag |
| Asp -13 | - | expression tag |
| Ile -12 | - | expression tag |
| Phe -11 | - | expression tag |
| Glu -10 | - | expression tag |
| Ala -9 | - | expression tag |
| Gln -8 | - | expression tag |
| Lys -7 | - | expression tag |
| Ile -6 | - | expression tag |
| Glu -5 | - | expression tag |
| Trp -4 | - | expression tag |
| His -3 | - | expression tag |
| Glu -2 | - | expression tag |
| Asp -1 | - | expression tag |
| Thr 0 | - | expression tag |
| Gly 1 | - | expression tag |
| Ser 2 | - | expression tag |
| Ser 3 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| His 172 | - | expression tag |
| His 173 | - | expression tag |
| His 174 | - | expression tag |
| His 175 | - | expression tag |
| His 176 | - | expression tag |
| His 177 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Lys 346 | - | expression tag |
| His 347 | - | expression tag |
| His 348 | - | expression tag |
| His 349 | - | expression tag |
| His 350 | - | expression tag |
| His 351 | - | expression tag |
| His 352 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Lys 241 | - | expression tag |
| His 242 | - | expression tag |
| His 243 | - | expression tag |
| His 244 | - | expression tag |
| His 245 | - | expression tag |
| His 246 | - | expression tag |
| His 247 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Pro -1 | - | expression tag |
| Gly 0 | - | expression tag |
| 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 |
| PDB | External Database | Details |
|---|---|---|
| Ala 483 | - | expression tag |
| Ala 484 | - | expression tag |
| Ala 485 | - | expression tag |
| Leu 486 | - | expression tag |
| Glu 487 | - | expression tag |
| His 488 | - | expression tag |
| His 489 | - | expression tag |
| His 490 | - | expression tag |
| His 491 | - | expression tag |
| His 492 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -3 | - | expression tag |
| Pro -2 | - | expression tag |
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Pro -1 | - | expression tag |
| His 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Ser -2 | - | expression tag |
| Asn -1 | - | expression tag |
| Ala 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -3 | - | expression tag |
| Pro -2 | - | expression tag |
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Gly -1 | - | expression tag |
| Ser 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Ala 102 | Gly 103 | conflict |
| Ala 110 | Cys 111 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Thr 29 | Ser 33 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 38 |
| Total formula weight | 1534185.6 | |
| Non-Polymers* | Number of molecules | 19 |
| Total formula weight | 1487.9 | |
| All* | Total formula weight | 1535673.5 |
