8GXS
PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
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 | X | DNA (228-mer) | polymer | 228 | 70328.7 | 1 | synthetic construct | Non-template DNA | |
| 2 | Y | DNA (228-mer) | polymer | 228 | 70483.8 | 1 | synthetic construct | Template DNA | |
| 3 | NX | DNA (162-mer) | polymer | 162 | 46802.4 | 1 | synthetic construct | Nucleosome DNA | |
| 4 | NY | DNA (162-mer) | polymer | 162 | 53286.5 | 1 | synthetic construct | Nucleosome DNA | |
| 5 | BA | Transcription initiation factor IIB | polymer | 316 | 34877.9 | 1 | UniProt (Q00403) Pfam (PF00382) Pfam (PF08271) In PDB | Homo sapiens (human) | General transcription factor TFIIB,S300-II |
| 6 | DA | Transcription initiation factor TFIID subunit 1 | polymer | 1872 | 212956.2 | 1 | UniProt (P21675) Pfam (PF09247) Pfam (PF00439) Pfam (PF12157) Pfam (PF15288) In PDB | Homo sapiens (human) | Cell cycle gene 1 protein,TBP-associated factor 250 kDa,p250,Transcription initiation factor TFIID 250 kDa subunit,TAF(II)250,TAFII-250,TAFII250 |
| 7 | EA | General transcription factor IIE subunit 1 | polymer | 439 | 49516.1 | 1 | UniProt (P29083) Pfam (PF02002) Pfam (PF08271) Pfam (PF11521) In PDB | Homo sapiens (human) | General transcription factor IIE 56 kDa subunit,Transcription initiation factor IIE subunit alpha,TFIIE-alpha |
| 8 | FA | General transcription factor IIF subunit 1 | polymer | 517 | 58343.6 | 1 | UniProt (P35269) Pfam (PF05793) In PDB | Homo sapiens (human) | General transcription factor IIF 74 kDa subunit,Transcription initiation factor IIF subunit alpha,TFIIF-alpha,Transcription initiation factor RAP74 |
| 9 | HA | General transcription and DNA repair factor IIH helicase subunit XPD | polymer | 760 | 87021.1 | 1 | UniProt (P18074) Pfam (PF06733) Pfam (PF06777) Pfam (PF13307) In PDB | Homo sapiens (human) | TFIIH subunit XPD,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 80 kDa subunit,TFIIH p80,Xeroderma pigmentosum group D-complementing protein |
| 10 | NA, NE | Histone H3 | polymer | 136 | 15435.1 | 2 | UniProt (A0A310TTQ1) Pfam (PF00125) In PDB | Xenopus laevis (African clawed frog) | |
| 11 | PA | DNA-directed RNA polymerase subunit | polymer | 1970 | 217450.1 | 1 | UniProt (A0A8D1DPV6) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) In PDB | Sus scrofa (pig) | |
| 12 | DB | Transcription initiation factor TFIID subunit 2 | polymer | 1199 | 137160.0 | 1 | UniProt (Q6P1X5) In PDB | Homo sapiens (human) | 150 kDa cofactor of initiator function,RNA polymerase II TBP-associated factor subunit B,TBP-associated factor 150 kDa,Transcription initiation factor TFIID 150 kDa subunit,TAF(II)150,TAFII-150,TAFII150 |
| 13 | EB | Transcription initiation factor IIE subunit beta | polymer | 291 | 33106.8 | 1 | UniProt (P29084) Pfam (PF02186) Pfam (PF18121) In PDB | Homo sapiens (human) | TFIIE-beta,General transcription factor IIE subunit 2 |
| 14 | FB | General transcription factor IIF subunit 2 | polymer | 249 | 28427.3 | 1 | UniProt (P13984) Pfam (PF17683) Pfam (PF02270) In PDB | 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 |
| 15 | HB | General transcription factor IIH subunit 1 | polymer | 548 | 62116.5 | 1 | UniProt (P32780) Pfam (PF08567) Pfam (PF03909) In PDB | 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 |
| 16 | NB, NF | Histone H4 | polymer | 103 | 11394.4 | 2 | UniProt (P62799) Pfam (PF15511) In PDB | Xenopus laevis (African clawed frog) | |
| 17 | PB | DNA-directed RNA polymerase subunit beta | polymer | 1174 | 134041.4 | 1 | UniProt (A0A4X1TVZ5) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) In PDB | Sus scrofa (pig) | |
| 18 | HC | General transcription factor IIH subunit 4 | polymer | 462 | 52245.2 | 1 | UniProt (Q92759) Pfam (PF03849) Pfam (PF18307) In PDB | 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 |
| 19 | DO | Transcription initiation factor IIA subunit 2 | polymer | 109 | 12469.1 | 1 | UniProt (P52657) Pfam (PF02268) Pfam (PF02751) In PDB | Homo sapiens (human) | General transcription factor IIA subunit 2,TFIIA p12 subunit,TFIIA-12,TFIIAS,Transcription initiation factor IIA gamma chain,TFIIA-gamma |
| 20 | DP | TATA-box-binding protein | polymer | 339 | 37729.9 | 1 | UniProt (P20226) Pfam (PF00352) In PDB | Homo sapiens (human) | TATA sequence-binding protein,TATA-binding factor,TATA-box factor,Transcription initiation factor TFIID TBP subunit |
| 21 | DQ | Transcription initiation factor IIA subunit 1 | polymer | 376 | 41544.6 | 1 | UniProt (P52655) Pfam (PF03153) In PDB | Homo sapiens (human) | General transcription factor IIA subunit 1,TFIIAL,Transcription initiation factor TFIIA 42 kDa subunit,TFIIA-42 |
| 22 | PC | DNA-directed RNA polymerase II subunit RPB3 | polymer | 275 | 31439.1 | 1 | UniProt (I3LCH3) Pfam (PF01193) Pfam (PF01000) In PDB | Sus scrofa (pig) | RNA polymerase II subunit C |
| 23 | PE | DNA-directed RNA polymerase II subunit E | polymer | 210 | 24644.3 | 1 | UniProt (A0A4X1VTX4) Pfam (PF03871) Pfam (PF01191) In PDB | Sus scrofa (pig) | RPB5 homolog |
| 24 | PF | DNA-directed RNA polymerase II subunit F | polymer | 127 | 14477.0 | 1 | UniProt (A0A4X1VEK9) Pfam (PF01192) In PDB | Sus scrofa (pig) | DNA-directed RNA polymerases I,II,and III subunit RPABC2,RPB6 homolog |
| 25 | PH | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 150 | 17162.3 | 1 | UniProt (A0A4X1ULF2) UniProt (by SIFTS) (I3LCB2) Pfam (PF03870) In PDB | Sus scrofa (pig) | |
| 26 | PI | DNA-directed RNA polymerase II subunit RPB9 | polymer | 125 | 14541.2 | 1 | UniProt (P60899) Pfam (PF02150) Pfam (PF01096) In PDB | Sus scrofa (pig) | RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5 |
| 27 | PJ | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 67 | 7655.1 | 1 | UniProt (A0A493TD97) Pfam (PF01194) In PDB | Sus scrofa (pig) | |
| 28 | PK | RNA_pol_L_2 domain-containing protein | polymer | 117 | 13310.3 | 1 | UniProt (A0A4X1UK25) UniProt (by SIFTS) (F1RKE4) Pfam (PF13656) In PDB | Sus scrofa (pig) | |
| 29 | PL | RPB12 | polymer | 58 | 7018.2 | 1 | UniProt (A0A4X1TRS6) Pfam (PF03604) In PDB | Sus scrofa (pig) | |
| 30 | HD | CDK-activating kinase assembly factor MAT1 | polymer | 309 | 35874.0 | 1 | UniProt (P51948) Pfam (PF17121) Pfam (PF06391) In PDB | 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 |
| 31 | HG | General transcription factor IIH subunit 2 | polymer | 395 | 44482.0 | 1 | UniProt (Q13888) Pfam (PF04056) Pfam (PF07975) In PDB | 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 |
| 32 | HE | General transcription factor IIH subunit 3 | polymer | 308 | 34416.0 | 1 | UniProt (Q13889) Pfam (PF03850) In PDB | 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 |
| 33 | HF | General transcription factor IIH subunit 5 | polymer | 71 | 8060.4 | 1 | UniProt (Q6ZYL4) Pfam (PF06331) In PDB | Homo sapiens (human) | General transcription factor IIH polypeptide 5,TFB5 ortholog,TFIIH basal transcription factor complex TTD-A subunit |
| 34 | HH | General transcription and DNA repair factor IIH helicase subunit XPB | polymer | 782 | 89404.7 | 1 | UniProt (P19447) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) In PDB | 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 89 kDa subunit,TFIIH p89,Xeroderma pigmentosum group B-complementing protein |
| 35 | DD, Dd | Transcription initiation factor TFIID subunit 4 | polymer | 1085 | 110221.9 | 2 | UniProt (O00268) Pfam (PF07531) Pfam (PF05236) In PDB | Homo sapiens (human) | RNA polymerase II TBP-associated factor subunit C,TBP-associated factor 4,Transcription initiation factor TFIID 130 kDa subunit,TAF(II)130,TAFII-130,TAFII130,Transcription initiation factor TFIID 135 kDa subunit,TAF(II)135,TAFII-135,TAFII135 |
| 36 | DE, De | Transcription initiation factor TFIID subunit 5 | polymer | 800 | 86932.1 | 2 | UniProt (Q15542) Pfam (PF04494) Pfam (PF00400) In PDB | Homo sapiens (human) | Transcription initiation factor TFIID 100 kDa subunit,TAF(II)100,TAFII-100,TAFII100 |
| 37 | DF, Df | Transcription initiation factor TFIID subunit 6 | polymer | 677 | 72749.3 | 2 | UniProt (P49848) Pfam (PF02969) Pfam (PF07571) In PDB | Homo sapiens (human) | RNA polymerase II TBP-associated factor subunit E,Transcription initiation factor TFIID 70 kDa subunit,TAF(II)70,TAFII-70,TAFII70,Transcription initiation factor TFIID 80 kDa subunit,TAF(II)80,TAFII-80,TAFII80 |
| 38 | DG | Transcription initiation factor TFIID subunit 7 | polymer | 349 | 40325.1 | 1 | UniProt (Q15545) Pfam (PF04658) In PDB | Homo sapiens (human) | RNA polymerase II TBP-associated factor subunit F,Transcription initiation factor TFIID 55 kDa subunit,TAF(II)55,TAFII-55,TAFII55 |
| 39 | DH | Transcription initiation factor TFIID subunit 8 | polymer | 310 | 34304.4 | 1 | UniProt (Q7Z7C8) Pfam (PF07524) Pfam (PF10406) In PDB | Homo sapiens (human) | Protein taube nuss,TBP-associated factor 43 kDa,TBP-associated factor 8,Transcription initiation factor TFIID 43 kDa subunit,TAFII-43,TAFII43,hTAFII43 |
| 40 | DI, Di | Transcription initiation factor TFIID subunit 9 | polymer | 264 | 29006.8 | 2 | UniProt (Q16594) Pfam (PF02291) In PDB | Homo sapiens (human) | RNA polymerase II TBP-associated factor subunit G,STAF31/32,Transcription initiation factor TFIID 31 kDa subunit,TAFII-31,TAFII31,Transcription initiation factor TFIID 32 kDa subunit,TAFII-32,TAFII32 |
| 41 | DL, Dl | Transcription initiation factor TFIID subunit 12 | polymer | 161 | 17948.5 | 2 | UniProt (Q16514) Pfam (PF03847) In PDB | Homo sapiens (human) | Transcription initiation factor TFIID 20/15 kDa subunits,TAFII-20/TAFII-15,TAFII20/TAFII15 |
| 42 | Dc | Transcription initiation factor TFIID subunit 3 | polymer | 929 | 103769.3 | 1 | UniProt (Q5VWG9) Pfam (PF07524) Pfam (PF00628) In PDB | Homo sapiens (human) | 140 kDa TATA box-binding protein-associated factor,TBP-associated factor 3,Transcription initiation factor TFIID 140 kDa subunit,TAF(II)140,TAF140,TAFII-140,TAFII140 |
| 43 | Dj, DJ | Transcription initiation factor TFIID subunit 10 | polymer | 218 | 21731.2 | 2 | UniProt (Q12962) Pfam (PF03540) In PDB | Homo sapiens (human) | STAF28,Transcription initiation factor TFIID 30 kDa subunit,TAF(II)30,TAFII-30,TAFII30 |
| 44 | Dk | Transcription initiation factor TFIID subunit 11 | polymer | 211 | 23340.1 | 1 | UniProt (Q15544) Pfam (PF04719) In PDB | Homo sapiens (human) | TFIID subunit p30-beta,Transcription initiation factor TFIID 28 kDa subunit,TAF(II)28,TAFII-28,TAFII28 |
| 45 | Dm | Transcription initiation factor TFIID subunit 13 | polymer | 124 | 14307.1 | 1 | UniProt (Q15543) Pfam (PF02269) In PDB | Homo sapiens (human) | Transcription initiation factor TFIID 18 kDa subunit,TAF(II)18,TAFII-18,TAFII18 |
| 46 | HI | Cyclin-dependent kinase 7 | polymer | 346 | 39032.2 | 1 | UniProt (P50613) Pfam (PF00069) In PDB | 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 |
| 47 | HJ | Cyclin-H | polymer | 323 | 37695.5 | 1 | UniProt (P51946) Pfam (PF00134) Pfam (PF16899) In PDB | Homo sapiens (human) | MO15-associated protein,p34,p37 |
| 48 | PD | DNA-directed RNA polymerase II subunit RPB4 | polymer | 142 | 16331.3 | 1 | UniProt (A0A481BYI6) Pfam (PF03874) In PDB | Sus scrofa (pig) | DNA-directed RNA polymerase II subunit RPB4 isoform X1 |
| 49 | PG | DNA-directed RNA polymerase II subunit RPB7 | polymer | 172 | 19314.3 | 1 | UniProt (A0A4X1VKG7) Pfam (PF03876) Pfam (PF00575) In PDB | Sus scrofa (pig) | |
| 50 | g | Mediator of RNA polymerase II transcription subunit 7 | polymer | 233 | 27285.3 | 1 | UniProt (O43513) Pfam (PF05983) In PDB | Homo sapiens (human) | |
| 51 | j | Mediator of RNA polymerase II transcription subunit 10 | polymer | 135 | 15711.0 | 1 | UniProt (Q9BTT4) Pfam (PF09748) In PDB | Homo sapiens (human) | |
| 52 | n | Mediator of RNA polymerase II transcription subunit 14 | polymer | 1454 | 160787.6 | 1 | UniProt (O60244) Pfam (PF08638) Pfam (PF22981) Pfam (PF22984) Pfam (PF22983) In PDB | Homo sapiens (human) | |
| 53 | s | Mediator of RNA polymerase II transcription subunit 19 | polymer | 244 | 26321.1 | 1 | UniProt (A0JLT2) Pfam (PF10278) In PDB | Homo sapiens (human) | |
| 54 | u | Mediator of RNA polymerase II transcription subunit 21 | polymer | 144 | 15575.2 | 1 | UniProt (Q13503) Pfam (PF11221) In PDB | Homo sapiens (human) | |
| 55 | a | Mediator of RNA polymerase II transcription subunit 1 | polymer | 1581 | 168697.3 | 1 | UniProt (Q15648) Pfam (PF10744) In PDB | Homo sapiens (human) | |
| 56 | d | Mediator of RNA polymerase II transcription subunit 4 | polymer | 270 | 29781.4 | 1 | UniProt (Q9NPJ6) Pfam (PF10018) In PDB | Homo sapiens (human) | |
| 57 | f | Mediator of RNA polymerase II transcription subunit 6 | polymer | 246 | 28464.6 | 1 | UniProt (O75586) Pfam (PF04934) In PDB | Homo sapiens (human) | |
| 58 | i | Mediator of RNA polymerase II transcription subunit 9 | polymer | 146 | 16422.8 | 1 | UniProt (Q9NWA0) Pfam (PF07544) In PDB | Homo sapiens (human) | |
| 59 | m | Mediator of RNA polymerase II transcription subunit 31 | polymer | 131 | 15826.1 | 1 | UniProt (Q9Y3C7) Pfam (PF05669) In PDB | Homo sapiens (human) | |
| 60 | q | Mediator of RNA polymerase II transcription subunit 17 | polymer | 651 | 72984.0 | 1 | UniProt (Q9NVC6) Pfam (PF10156) In PDB | Homo sapiens (human) | |
| 61 | z | Mediator of RNA polymerase II transcription subunit 26 | polymer | 600 | 65544.4 | 1 | UniProt (O95402) Pfam (PF08711) Pfam (PF15694) Pfam (PF15693) In PDB | Homo sapiens (human) | |
| 62 | b | Mediator of RNA polymerase II transcription subunit 29 | polymer | 200 | 21089.8 | 1 | UniProt (Q9NX70) Pfam (PF11568) In PDB | Homo sapiens (human) | |
| 63 | c | Mediator of RNA polymerase II transcription subunit 27 | polymer | 311 | 35478.7 | 1 | UniProt (Q6P2C8) Pfam (PF11571) In PDB | Homo sapiens (human) | |
| 64 | e | Mediator of RNA polymerase II transcription subunit 28 | polymer | 178 | 19540.1 | 1 | UniProt (Q9H204) Pfam (PF11594) In PDB | Homo sapiens (human) | |
| 65 | l | Mediator of RNA polymerase II transcription subunit 30 | polymer | 178 | 20301.2 | 1 | UniProt (Q96HR3) Pfam (PF11315) In PDB | Homo sapiens (human) | |
| 66 | o | Mediator of RNA polymerase II transcription subunit 15 | polymer | 788 | 86830.1 | 1 | UniProt (Q96RN5) Pfam (PF09606) Pfam (PF21538) Pfam (PF21539) In PDB | Homo sapiens (human) | |
| 67 | h | Isoform 2 of Mediator of RNA polymerase II transcription subunit 8 | polymer | 268 | 29112.9 | 1 | UniProt (Q96G25) Pfam (PF10232) In PDB | Homo sapiens (human) | |
| 68 | k | Mediator of RNA polymerase II transcription subunit 11 | polymer | 117 | 13145.8 | 1 | UniProt (Q9P086) Pfam (PF10280) In PDB | Homo sapiens (human) | |
| 69 | r | Mediator of RNA polymerase II transcription subunit 18 | polymer | 208 | 23693.7 | 1 | UniProt (Q9BUE0) Pfam (PF09637) In PDB | Homo sapiens (human) | |
| 70 | t | Mediator of RNA polymerase II transcription subunit 20 | polymer | 212 | 23243.8 | 1 | UniProt (Q9H944) Pfam (PF08612) In PDB | Homo sapiens (human) | |
| 71 | v | Mediator of RNA polymerase II transcription subunit 22 | polymer | 200 | 22243.7 | 1 | UniProt (Q15528) Pfam (PF06179) In PDB | Homo sapiens (human) | |
| 72 | p | Isoform 2 of Mediator of RNA polymerase II transcription subunit 16 | polymer | 841 | 93136.0 | 1 | UniProt (Q9Y2X0) Pfam (PF00400) Pfam (PF11635) Pfam (PF20718) Pfam (PF20719) In PDB | Homo sapiens (human) | |
| 73 | w | Mediator of RNA polymerase II transcription subunit 23 | polymer | 1368 | 156652.2 | 1 | UniProt (Q9ULK4) Pfam (PF11573) In PDB | Homo sapiens (human) | |
| 74 | x | Mediator of RNA polymerase II transcription subunit 24 | polymer | 989 | 110430.2 | 1 | UniProt (O75448) Pfam (PF11277) In PDB | Homo sapiens (human) | |
| 75 | y | Mediator of RNA polymerase II transcription subunit 25 | polymer | 747 | 78230.3 | 1 | UniProt (Q71SY5) Pfam (PF11265) Pfam (PF11235) Pfam (PF11232) In PDB | Homo sapiens (human) | |
| 76 | NC, NG | HISTONE H2A.Z | polymer | 128 | 13581.8 | 2 | Homo sapiens | ||
| 77 | ND, NH | Histone H2B | polymer | 126 | 13979.3 | 2 | UniProt (A0A8J0U496) Pfam (PF00125) In PDB | Xenopus laevis (African clawed frog) | |
| 78 | HE, c, p, BA, EA... | ZINC ION | non-polymer | 65.4 | 19 | Chemie (ZN) | |||
| 79 | HA | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 1 | Chemie (SF4) | |||
| 80 | PA | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
HI: 1 - 346 (UniProt: P50613)
| PDB | External Database | Details |
|---|---|---|
| Ala 41 | Lys 41 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 87 |
| Total formula weight | 4273301.4 | |
| Non-Polymers* | Number of molecules | 21 |
| Total formula weight | 1618.7 | |
| All* | Total formula weight | 4274920.2 |
