7ZSA
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B)
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 (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) 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 | 347 | 38635.9 | 1 | UniProt (P16370) Pfam (PF01193) Pfam (PF01000) In PDB | Saccharomyces cerevisiae (baker's yeast) | RNA polymerase II subunit 3,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 | 177 | 19909.9 | 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 | Transcription initiation factor IIB | polymer | 352 | 39215.4 | 1 | UniProt (P29055) Pfam (PF08271) Pfam (PF00382) In PDB | Saccharomyces cerevisiae (baker's yeast) | General transcription factor TFIIB,Transcription factor E |
14 | N | Non-template DNA (209-MER) | polymer | 209 | 64291.0 | 1 | synthetic construct | ||
15 | O | TATA-box-binding protein | polymer | 247 | 28000.3 | 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 |
16 | Q | Transcription initiation factor IIF subunit alpha | polymer | 738 | 82531.8 | 1 | UniProt (P41895) Pfam (PF05793) In PDB | Saccharomyces cerevisiae (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 (baker's yeast) | TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit |
18 | T | Template DNA (209-MER) | polymer | 209 | 64754.3 | 1 | synthetic construct | ||
19 | U | Transcription initiation factor IIA large subunit | polymer | 171 | 19432.0 | 1 | Pfam (PF03153) UniProt (by SIFTS) (P32773) In PDB | Saccharomyces cerevisiae | |
20 | V | Transcription initiation factor IIA subunit 2 | polymer | 129 | 14431.1 | 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 |
21 | W | Transcription initiation factor IIE subunit alpha | polymer | 492 | 55951.0 | 1 | UniProt (P36100) Pfam (PF02002) In PDB | Saccharomyces cerevisiae (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 (baker's yeast) | TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit |
23 | 0 | General transcription and DNA repair factor IIH helicase subunit XPD | polymer | 778 | 89899.0 | 1 | UniProt (P06839) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) In PDB | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3 |
24 | 1 | General transcription and DNA repair factor IIH subunit TFB1 | polymer | 645 | 73194.5 | 1 | UniProt (P32776) Pfam (PF08567) Pfam (PF03909) In PDB | 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 | 2 | General transcription and DNA repair factor IIH subunit TFB2 | polymer | 517 | 58900.6 | 1 | UniProt (Q02939) Pfam (PF03849) Pfam (PF18307) In PDB | 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 | 3 | RNA polymerase II transcription factor B subunit 3 | polymer | 324 | 38480.7 | 1 | UniProt (Q03290) Pfam (PF06391) Pfam (PF17121) In PDB | Saccharomyces cerevisiae (baker's yeast) | RNA polymerase II transcription factor B 38 kDa subunit,RNA polymerase II transcription factor B p38 subunit |
27 | 4 | General transcription and DNA repair factor IIH subunit TFB4 | polymer | 341 | 37778.7 | 1 | UniProt (Q12004) Pfam (PF03850) In PDB | 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 | 5 | General transcription and DNA repair factor IIH subunit TFB5 | polymer | 76 | 8541.8 | 1 | UniProt (Q3E7C1) Pfam (PF06331) In PDB | Saccharomyces cerevisiae (baker's yeast) | TFIIH subunit TFB5,RNA polymerase II transcription factor B subunit 5 |
29 | 6 | General transcription and DNA repair factor IIH subunit SSL1 | polymer | 464 | 52571.2 | 1 | UniProt (Q04673) Pfam (PF04056) Pfam (PF07975) In PDB | 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 | 7 | General transcription and DNA repair factor IIH helicase subunit XPB | polymer | 843 | 95461.7 | 1 | UniProt (Q00578) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) In PDB | 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 | a, e | Histone H3.2 | polymer | 135 | 15271.9 | 2 | UniProt (P84233) Pfam (PF00125) In PDB | Xenopus laevis (African clawed frog) | |
32 | b, f | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (P62799) Pfam (PF15511) In PDB | Xenopus laevis (African clawed frog) | |
33 | c, g | Histone H2A | polymer | 129 | 13978.2 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) UniProt (by SIFTS) (P06897) In PDB | Xenopus laevis (African clawed frog) | |
34 | d, h | Histone H2B 1.1 | polymer | 125 | 13848.1 | 2 | UniProt (P02281) Pfam (PF00125) In PDB | Xenopus laevis (African clawed frog) | H2B1.1 |
35 | 4, 6, A, B, C... | ZINC ION | non-polymer | 65.4 | 17 | Chemie (ZN) | |||
36 | A | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
37 | 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 |