8BYQ
RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W)
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (0) | General transcription and DNA repair factor IIH helicase subunit XPB | polymer | 782 | 89404.7 | 1 | UniProt (P19447) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) | Homo sapiens (human) | TFIIH subunit XPB,Basic transcription factor 2 89 kDa subunit,BTF2 p89,DNA excision repair protein ERCC-3,DNA repair protein complementing XP-B cells,TFIIH basal transcription factor complex 89 kDa subunit,TFIIH p89,Xeroderma pigmentosum group B-complementing protein |
| 2 | B (1) | TFIIH basal transcription factor complex helicase XPD subunit | polymer | 760 | 87021.1 | 1 | UniProt (P18074) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) | Homo sapiens (human) | Basic transcription factor 2 80 kDa subunit,BTF2 p80,CXPD,DNA excision repair protein ERCC-2,DNA repair protein complementing XP-D cells,TFIIH basal transcription factor complex 80 kDa subunit,TFIIH p80,Xeroderma pigmentosum group D-complementing protein |
| 3 | C (2) | General transcription factor IIH subunit 1 | polymer | 548 | 62116.5 | 1 | UniProt (P32780) Pfam (PF08567) Pfam (PF03909) | Homo sapiens (human) | Basic transcription factor 2 62 kDa subunit,BTF2 p62,General transcription factor IIH polypeptide 1,TFIIH basal transcription factor complex p62 subunit |
| 4 | D (3) | General transcription factor IIH subunit 4 | polymer | 462 | 52245.2 | 1 | UniProt (Q92759) Pfam (PF18307) Pfam (PF03849) | Homo sapiens (human) | Basic transcription factor 2 52 kDa subunit,BTF2 p52,General transcription factor IIH polypeptide 4,TFIIH basal transcription factor complex p52 subunit |
| 5 | E (4) | General transcription factor IIH subunit 2 | polymer | 395 | 44482.0 | 1 | UniProt (Q13888) Pfam (PF04056) Pfam (PF07975) | Homo sapiens (human) | Basic transcription factor 2 44 kDa subunit,BTF2 p44,General transcription factor IIH polypeptide 2,TFIIH basal transcription factor complex p44 subunit |
| 6 | F (5) | General transcription factor IIH subunit 3 | polymer | 308 | 34416.0 | 1 | UniProt (Q13889) Pfam (PF03850) | Homo sapiens (human) | Basic transcription factor 2 34 kDa subunit,BTF2 p34,General transcription factor IIH polypeptide 3,TFIIH basal transcription factor complex p34 subunit |
| 7 | G (6) | General transcription factor IIH subunit 5 | polymer | 71 | 8060.4 | 1 | UniProt (Q6ZYL4) Pfam (PF06331) | Homo sapiens (human) | General transcription factor IIH polypeptide 5,TFB5 ortholog,TFIIH basal transcription factor complex TTD-A subunit |
| 8 | H (7) | CDK-activating kinase assembly factor MAT1 | polymer | 309 | 35874.0 | 1 | UniProt (P51948) Pfam (PF17121) Pfam (PF06391) | Homo sapiens (human) | CDK7/cyclin-H assembly factor,Cyclin-G1-interacting protein,Menage a trois,RING finger protein 66,RING finger protein MAT1,p35,p36 |
| 9 | I (8) | Cyclin-dependent kinase 7 | polymer | 346 | 39090.3 | 1 | UniProt (P50613) Pfam (PF00069) | Homo sapiens (human) | 39 kDa protein kinase,p39 Mo15,CDK-activating kinase 1,Cell division protein kinase 7,Serine/threonine-protein kinase 1,TFIIH basal transcription factor complex kinase subunit |
| 10 | J (9) | Cyclin-H | polymer | 323 | 37695.5 | 1 | UniProt (P51946) Pfam (PF00134) Pfam (PF16899) | Homo sapiens (human) | MO15-associated protein,p34,p37 |
| 11 | K (A) | DNA-directed RNA polymerase subunit | polymer | 1970 | 217450.1 | 1 | UniProt (A0A7M4DUC2) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) | Sus scrofa (pig) | |
| 12 | L (B) | DNA-directed RNA polymerase subunit beta | polymer | 1174 | 134041.4 | 1 | UniProt (I3LGP4) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) | Sus scrofa (pig) | |
| 13 | M (C) | DNA-directed RNA polymerase II subunit RPB3 | polymer | 275 | 31439.1 | 1 | UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) | Sus scrofa (pig) | |
| 14 | N (D) | RNA polymerase II subunit D | polymer | 142 | 16331.3 | 1 | UniProt (A0A287ADR4) Pfam (PF03874) | Sus scrofa (pig) | |
| 15 | O (E) | DNA-directed RNA polymerase II subunit E | polymer | 210 | 24644.3 | 1 | UniProt (I3LSI7) Pfam (PF03871) Pfam (PF01191) | Sus scrofa (pig) | RPB5 homolog |
| 16 | P (F) | DNA-directed RNA polymerase II subunit F | polymer | 127 | 14477.0 | 1 | UniProt (F1SKN8) Pfam (PF01192) UniProt (by SIFTS) (A0A4X1VEK9) | Sus scrofa (pig) | DNA-directed RNA polymerases I,II,and III subunit RPABC2,RPB6 homolog |
| 17 | Q (G) | DNA-directed RNA polymerase II subunit RPB7 | polymer | 172 | 19314.3 | 1 | UniProt (A0A4X1VKG7) Pfam (PF03876) Pfam (PF00575) | Sus scrofa (pig) | |
| 18 | R (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 150 | 17162.3 | 1 | UniProt (I3LCB2) Pfam (PF03870) | Sus scrofa (pig) | |
| 19 | S (I) | DNA-directed RNA polymerase II subunit RPB9 | polymer | 125 | 14541.2 | 1 | UniProt (P60899) Pfam (PF02150) Pfam (PF01096) | Sus scrofa (pig) | RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5 |
| 20 | T (J) | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 67 | 7655.1 | 1 | UniProt (A0A4X1VYD0) Pfam (PF01194) | Sus scrofa (pig) | |
| 21 | U (K) | DNA-directed RNA polymerase II subunit RPB11-a | polymer | 117 | 13310.3 | 1 | UniProt (F1RKE4) Pfam (PF13656) | Sus scrofa (pig) | |
| 22 | V (L) | RNA polymerase II subunit K | polymer | 58 | 7018.2 | 1 | UniProt (I3LN51) Pfam (PF03604) UniProt (by SIFTS) (A0A4X1TRS6) | Sus scrofa (pig) | |
| 23 | W (M) | Transcription initiation factor IIB | polymer | 316 | 34877.9 | 1 | UniProt (Q00403) Pfam (PF08271) Pfam (PF00382) | Homo sapiens (human) | General transcription factor TFIIB,S300-II |
| 24 | X (N) | Non-template DNA | polymer | 210 | 64775.2 | 1 | unidentified adenovirus | ||
| 25 | Y (O) | TATA-box-binding protein | polymer | 339 | 37729.9 | 1 | UniProt (P20226) Pfam (PF00352) | Homo sapiens (human) | TATA sequence-binding protein,TATA-binding factor,TATA-box factor,Transcription initiation factor TFIID TBP subunit |
| 26 | Z (Q) | General transcription factor IIF subunit 1 | polymer | 517 | 58343.6 | 1 | UniProt (P35269) Pfam (PF05793) | Homo sapiens (human) | General transcription factor IIF 74 kDa subunit,Transcription initiation factor IIF subunit alpha,TFIIF-alpha,Transcription initiation factor RAP74 |
| 27 | AA (R) | General transcription factor IIF subunit 2 | polymer | 249 | 28427.3 | 1 | UniProt (P13984) Pfam (PF17683) Pfam (PF02270) | Homo sapiens (human) | ATP-dependent helicase GTF2F2,General transcription factor IIF 30 kDa subunit,Transcription initiation factor IIF subunit beta,TFIIF-beta,Transcription initiation factor RAP30 |
| 28 | BA (T) | Template DNA | polymer | 210 | 64909.3 | 1 | unidentified adenovirus | ||
| 29 | CA (U) | Transcription initiation factor IIA subunit 1 | polymer | 376 | 41544.6 | 1 | UniProt (P52655) Pfam (PF03153) | Homo sapiens (human) | General transcription factor IIA subunit 1,TFIIAL,Transcription initiation factor TFIIA 42 kDa subunit,TFIIA-42 |
| 30 | DA (V) | Transcription initiation factor IIA subunit 2 | polymer | 109 | 12469.1 | 1 | UniProt (P52657) Pfam (PF02268) Pfam (PF02751) | Homo sapiens (human) | General transcription factor IIA subunit 2,TFIIA p12 subunit,TFIIA-12,TFIIAS,Transcription initiation factor IIA gamma chain,TFIIA-gamma |
| 31 | EA (W) | General transcription factor IIE subunit 1 | polymer | 196 | 22922.3 | 1 | UniProt (P29083) Pfam (PF02002) Pfam (PF08271) | Homo sapiens (human) | General transcription factor IIE 56 kDa subunit,Transcription initiation factor IIE subunit alpha,TFIIE-alpha |
| 32 | FA (X) | Transcription initiation factor IIE subunit beta | polymer | 291 | 33106.8 | 1 | UniProt (P29084) Pfam (PF02186) Pfam (PF18121) | Homo sapiens (human) | TFIIE-beta,General transcription factor IIE subunit 2 |
| 33 | GA, KA (a, e) | Histone H3.2 | polymer | 136 | 15435.1 | 2 | UniProt (P84233) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 34 | HA, LA (b, f) | Histone H4 | polymer | 103 | 11394.4 | 2 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 35 | IA, MA (c, g) | Histone H2A type 1 | polymer | 130 | 14093.4 | 2 | UniProt (P06897) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 36 | JA, NA (d, h) | Histone H2B 1.1 | polymer | 126 | 13965.3 | 2 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 37 | OA (1) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 1 | Chemie (SF4) | |||
| 38 | AB, BB, CB, DB, EB... (I, J, L, M, W...) | ZINC ION | non-polymer | 65.4 | 16 | Chemie (ZN) | |||
| 39 | XA (A) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
A: 1 - 1970 (UniProt: A0A7M4DUC2)
a, e: 1 - 136 (UniProt: P84233)
c, g: 1 - 130 (UniProt: P06897)
| PDB | External Database | Details |
|---|---|---|
| - | Tyr 1636 | deletion |
| - | Ser 1637 | deletion |
| - | Pro 1638 | deletion |
| - | Thr 1639 | deletion |
| - | Ser 1640 | deletion |
| - | Pro 1641 | deletion |
| - | Ser 1642 | deletion |
| - | Tyr 1643 | deletion |
| - | Ser 1644 | deletion |
| - | Pro 1645 | deletion |
| - | Thr 1646 | deletion |
| - | Ser 1647 | deletion |
| - | Pro 1648 | deletion |
| - | Ser 1649 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Ala 103 | Gly 103 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Arg 100 | Gly 100 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 40 |
| Total formula weight | 1516672.7 | |
| Non-Polymers* | Number of molecules | 18 |
| Total formula weight | 1422.5 | |
| All* | Total formula weight | 1518095.2 |
