7LBM
Structure of the human Mediator-bound transcription pre-initiation complex
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) | 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) | Homo sapiens (Human) | Mediator complex subunit 16,Thyroid hormone receptor-associated protein 5,Thyroid hormone receptor-associated protein complex 95 kDa component,Trap95,Vitamin D3 receptor-interacting protein complex 92 kDa component,DRIP92 |
| 2 | B (1) | Mediator of RNA polymerase II transcription subunit 23 | polymer | 1368 | 156652.2 | 1 | UniProt (Q9ULK4) Pfam (PF11573) | Homo sapiens (Human) | Activator-recruited cofactor 130 kDa component,ARC130,Cofactor required for Sp1 transcriptional activation subunit 3,CRSP complex subunit 3,Mediator complex subunit 23,Protein sur-2 homolog,hSur-2,Transcriptional coactivator CRSP130,Vitamin D3 receptor-interacting protein complex 130 kDa component,DRIP130 |
| 3 | C (2) | Mediator of RNA polymerase II transcription subunit 24 | polymer | 989 | 110430.2 | 1 | UniProt (O75448) Pfam (PF11277) | Homo sapiens (Human) | Activator-recruited cofactor 100 kDa component,ARC100,Cofactor required for Sp1 transcriptional activation subunit 4,CRSP complex subunit 4,Mediator complex subunit 24,Thyroid hormone receptor-associated protein 4,Thyroid hormone receptor-associated protein complex 100 kDa component,Trap100,hTRAP100,Vitamin D3 receptor-interacting protein complex 100 kDa component,DRIP100 |
| 4 | D (3) | Mediator of RNA polymerase II transcription subunit 25 | polymer | 747 | 78230.3 | 1 | UniProt (Q71SY5) Pfam (PF11265) Pfam (PF11235) Pfam (PF11232) | Homo sapiens (Human) | Activator interaction domain-containing protein 1,Activator-recruited cofactor 92 kDa component,ARC92,Mediator complex subunit 25,p78 |
| 5 | E (A) | DNA-directed RNA polymerase II subunit RPB1 | polymer | 1970 | 217420.0 | 1 | UniProt (P24928) Pfam (PF04997) Pfam (PF00623) Pfam (PF04983) Pfam (PF05000) Pfam (PF04998) Pfam (PF04992) Pfam (PF04990) Pfam (PF05001) | Homo sapiens (Human) | RNA polymerase II subunit B1, DNA-directed RNA polymerase II subunit A, DNA-directed RNA polymerase III largest subunit, RNA-directed RNA polymerase II subunit RPB1 |
| 6 | F (B) | DNA-directed RNA polymerase II subunit RPB2 | polymer | 1174 | 134071.5 | 1 | UniProt (P30876) Pfam (PF04563) Pfam (PF04561) Pfam (PF04565) Pfam (PF04566) Pfam (PF04567) Pfam (PF00562) Pfam (PF04560) | Homo sapiens (Human) | DNA-directed RNA polymerase II 140 kDa polypeptide,DNA-directed RNA polymerase II subunit B,RNA polymerase II subunit 2,RNA polymerase II subunit B2 |
| 7 | G (C) | DNA-directed RNA polymerase II subunit RPB3 | polymer | 275 | 31478.1 | 1 | UniProt (P19387) Pfam (PF01193) Pfam (PF01000) | Homo sapiens (Human) | RNA polymerase II subunit B3,DNA-directed RNA polymerase II 33 kDa polypeptide,RPB33,DNA-directed RNA polymerase II subunit C,RPB31 |
| 8 | H (D) | DNA-directed RNA polymerase II subunit RPB4 | polymer | 142 | 16331.3 | 1 | UniProt (O15514) Pfam (PF03874) | Homo sapiens (Human) | RNA polymerase II subunit B4,DNA-directed RNA polymerase II subunit D,RNA polymerase II 16 kDa subunit,RPB16 |
| 9 | I (E) | DNA-directed RNA polymerase II subunit RPB5 | polymer | 210 | 24584.2 | 1 | UniProt (P19388) Pfam (PF03871) Pfam (PF01191) | Homo sapiens (Human) | RNA polymerases I,II,and III subunit ABC1, DNA-directed RNA DNA-directed RNA polymerases I, II, and III subunit RPABC1, polymerase II 23 kDa polypeptide, DNA-directed RNA polymerase II subunit E, XAP4 |
| 10 | J (F) | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | polymer | 127 | 14491.0 | 1 | UniProt (P61218) Pfam (PF01192) | Homo sapiens (Human) | RNA polymerases I,II,and III subunit ABC2,DNA-directed RNA polymerase II subunit F,DNA-directed RNA polymerases I,and III 14.4 kDa polypeptide,RPABC14.4,RPB14.4,RPB6 homolog,RPC15 |
| 11 | K (G) | DNA-directed RNA polymerase II subunit RPB7 | polymer | 172 | 19314.3 | 1 | UniProt (P62487) Pfam (PF03876) Pfam (PF00575) | Homo sapiens (Human) | RNA polymerase II subunit B7,DNA-directed RNA polymerase II subunit G,RNA polymerase II 19 kDa subunit,RPB19 |
| 12 | L (H) | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | polymer | 150 | 17162.3 | 1 | UniProt (P52434) Pfam (PF03870) | Homo sapiens (Human) | RNA polymerases I,II,and III subunit ABC3,DNA-directed RNA polymerase II subunit H,DNA-directed RNA polymerases I,and III 17.1 kDa polypeptide,RPB17,RPB8 homolog,hRPB8 |
| 13 | M (I) | DNA-directed RNA polymerase II subunit RPB9 | polymer | 125 | 14541.2 | 1 | UniProt (P36954) Pfam (PF02150) Pfam (PF01096) | Homo sapiens (Human) | RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5 |
| 14 | N (J) | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | polymer | 67 | 7655.1 | 1 | UniProt (P62875) Pfam (PF01194) | Homo sapiens (Human) | RNA polymerases I,II,and III subunit ABC5,DNA-directed RNA polymerase III subunit L,RNA polymerase II 7.6 kDa subunit,RPB7.6,RPB10 homolog |
| 15 | O (K) | DNA-directed RNA polymerase II subunit RPB11-a | polymer | 117 | 13310.3 | 1 | UniProt (P52435) Pfam (PF13656) | Homo sapiens (Human) | RPB11a,DNA-directed RNA polymerase II subunit J-1,RNA polymerase II 13.3 kDa subunit |
| 16 | P (L) | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | polymer | 58 | 7018.2 | 1 | UniProt (P53803) Pfam (PF03604) | Homo sapiens (Human) | RNA polymerases I,II,and III subunit ABC4,ABC10-alpha,DNA-directed RNA polymerase II subunit K,RNA polymerase II 7.0 kDa subunit,RPB7.0,RPB10alpha |
| 17 | Q (M) | 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 |
| 18 | R (N) | 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,TFIIAS,Transcription initiation factor IIA gamma chain,TFIIA-gamma |
| 19 | S (O) | Transcription initiation factor IIB | polymer | 316 | 34877.9 | 1 | UniProt (Q00403) Pfam (PF08271) Pfam (PF00382) | Homo sapiens (Human) | General transcription factor TFIIB,S300-II |
| 20 | T (P) | 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 |
| 21 | U (Q) | General transcription factor IIE subunit 1 | polymer | 439 | 49516.1 | 1 | UniProt (P29083) Pfam (PF02002) Pfam (PF08271) Pfam (PF11521) | Homo sapiens (Human) | General transcription factor IIE 56 kDa subunit,Transcription initiation factor IIE subunit alpha,TFIIE-alpha |
| 22 | V (R) | 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 |
| 23 | W (S) | 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 |
| 24 | X (T) | 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 |
| 25 | Y (U) | super core promoter sense strand | polymer | 100 | 31002.8 | 1 | Homo sapiens | ||
| 26 | Z (V) | super core promoter antisense strand | polymer | 100 | 30708.5 | 1 | Homo sapiens | ||
| 27 | AA (W) | TFIIH basal transcription factor complex helicase XPB subunit | polymer | 782 | 89404.7 | 1 | UniProt (P19447) Pfam (PF13625) Pfam (PF04851) Pfam (PF16203) | Homo sapiens (Human) | 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 |
| 28 | BA (X) | 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 |
| 29 | CA (Y) | 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 |
| 30 | DA (Z) | General transcription factor IIH subunit 4, p52 | polymer | 462 | 52245.2 | 1 | UniProt (Q92759) Pfam (PF03849) Pfam (PF18307) | 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 |
| 31 | EA (a) | General transcription factor IIH subunit 2 | polymer | 395 | 44482.0 | 1 | UniProt (Q13888) Pfam (PF07975) Pfam (PF04056) | 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 | FA (b) | General transcription factor IIH subunit 3 | polymer | 308 | 34416.0 | 1 | UniProt (Q13889) Pfam (PF03850) | Homo sapiens (Human) | p34, Basic transcription factor 2 44 kDa subunit, BTF2 p44, General transcription factor IIH polypeptide 2, TFIIH basal transcription factor complex p44 subunit |
| 33 | GA (c) | 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 |
| 34 | HA (d) | CDK-activating kinase assembly factor MAT1 | polymer | 309 | 35874.0 | 1 | UniProt (P51948) Pfam (PF17121) Pfam (PF06391) Pfam (PF25811) | 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 |
| 35 | IA (e) | 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 |
| 36 | JA (f) | Cyclin-H | polymer | 323 | 37695.5 | 1 | UniProt (P51946) Pfam (PF00134) Pfam (PF16899) | Homo sapiens (Human) | MO15-associated protein,p34,p37 |
| 37 | KA (g) | Mediator of RNA polymerase II transcription subunit 6 | polymer | 246 | 28464.6 | 1 | UniProt (O75586) Pfam (PF04934) | Homo sapiens (Human) | Activator-recruited cofactor 33 kDa component,ARC33,Mediator complex subunit 6,hMed6,Renal carcinoma antigen NY-REN-28 |
| 38 | LA (h) | Mediator of RNA polymerase II transcription subunit 8 | polymer | 268 | 29112.9 | 1 | UniProt (Q96G25) Pfam (PF10232) | Homo sapiens (Human) | Activator-recruited cofactor 32 kDa component,ARC32,Mediator complex subunit 8 |
| 39 | MA (i) | Mediator of RNA polymerase II transcription subunit 11 | polymer | 117 | 13145.8 | 1 | UniProt (Q9P086) Pfam (PF10280) | Homo sapiens (Human) | Mediator complex subunit 11 |
| 40 | NA (j) | Mediator of RNA polymerase II transcription subunit 17 | polymer | 651 | 72984.0 | 1 | UniProt (Q9NVC6) Pfam (PF10156) | Homo sapiens (Human) | Activator-recruited cofactor 77 kDa component,ARC77,Cofactor required for Sp1 transcriptional activation subunit 6,CRSP complex subunit 6,Mediator complex subunit 17,Thyroid hormone receptor-associated protein complex 80 kDa component,Trap80,Transcriptional coactivator CRSP77,Vitamin D3 receptor-interacting protein complex 80 kDa component,DRIP80 |
| 41 | OA (k) | Mediator of RNA polymerase II transcription subunit 18 | polymer | 208 | 23693.7 | 1 | UniProt (Q9BUE0) Pfam (PF09637) | Homo sapiens (Human) | Mediator complex subunit 18,p28b |
| 42 | PA (l) | Mediator of RNA polymerase II transcription subunit 20 | polymer | 212 | 23243.8 | 1 | UniProt (Q9H944) Pfam (PF08612) | Homo sapiens (Human) | Mediator complex subunit 20,TRF-proximal protein homolog,hTRFP |
| 43 | QA (m) | Mediator of RNA polymerase II transcription subunit 22 | polymer | 200 | 22243.7 | 1 | UniProt (Q15528) Pfam (PF06179) | Homo sapiens (Human) | Mediator complex subunit 22,Surfeit locus protein 5,Surf-5 |
| 44 | RA (n) | Mediator of RNA polymerase II transcription subunit 27 | polymer | 311 | 35478.7 | 1 | UniProt (Q6P2C8) Pfam (PF11571) | Homo sapiens (Human) | Cofactor required for Sp1 transcriptional activation subunit 8,CRSP complex subunit 8,Mediator complex subunit 27,P37 TRAP/SMCC/PC2 subunit,Transcriptional coactivator CRSP34 |
| 45 | SA (o) | Mediator of RNA polymerase II transcription subunit 28 | polymer | 178 | 19540.1 | 1 | UniProt (Q9H204) Pfam (PF11594) | Homo sapiens (Human) | Endothelial-derived protein 1,Mediator complex subunit 28,Merlin and Grb2-interacting cytoskeletal protein,Magicin,Tumor angiogenesis marker EG-1 |
| 46 | TA (p) | Mediator of RNA polymerase II transcription subunit 29 | polymer | 200 | 21089.8 | 1 | UniProt (Q9NX70) Pfam (PF11568) | Homo sapiens (Human) | Intersex-like protein,Mediator complex subunit 29 |
| 47 | UA (q) | Mediator of RNA polymerase II transcription subunit 30 | polymer | 178 | 20301.2 | 1 | UniProt (Q96HR3) Pfam (PF11315) | Homo sapiens (Human) | Mediator complex subunit 30,TRAP/Mediator complex component TRAP25,Thyroid hormone receptor-associated protein 6,Thyroid hormone receptor-associated protein complex 25 kDa component,Trap25 |
| 48 | VA (r) | Mediator of RNA polymerase II transcription subunit 14 | polymer | 1454 | 160787.6 | 1 | UniProt (O60244) Pfam (PF08638) Pfam (PF22981) Pfam (PF25065) Pfam (PF25067) Pfam (PF22984) Pfam (PF22983) Pfam (PF25069) | Homo sapiens (Human) | Activator-recruited cofactor 150 kDa component,ARC150,Cofactor required for Sp1 transcriptional activation subunit 2,CRSP complex subunit 2,Mediator complex subunit 14,RGR1 homolog,hRGR1,Thyroid hormone receptor-associated protein complex 170 kDa component,Trap170,Transcriptional coactivator CRSP150,Vitamin D3 receptor-interacting protein complex 150 kDa component,DRIP150 |
| 49 | WA (s) | Mediator of RNA polymerase II transcription subunit 4 | polymer | 270 | 29781.4 | 1 | UniProt (Q9NPJ6) Pfam (PF10018) | Homo sapiens (Human) | Activator-recruited cofactor 36 kDa component,ARC36,Mediator complex subunit 4,TRAP/SMCC/PC2 subunit p36 subunit,Vitamin D3 receptor-interacting protein complex 36 kDa component,DRIP36 |
| 50 | XA (t) | Mediator of RNA polymerase II transcription subunit 7 | polymer | 233 | 27285.3 | 1 | UniProt (O43513) Pfam (PF05983) | Homo sapiens (Human) | hMED7,Activator-recruited cofactor 34 kDa component,ARC34,Cofactor required for Sp1 transcriptional activation subunit 9,CRSP complex subunit 9,Mediator complex subunit 7,RNA polymerase transcriptional regulation mediator subunit 7 homolog,Transcriptional coactivator CRSP33 |
| 51 | YA (u) | Mediator of RNA polymerase II transcription subunit 9 | polymer | 146 | 16422.8 | 1 | UniProt (Q9NWA0) Pfam (PF07544) | Homo sapiens (Human) | Mediator complex subunit 9 |
| 52 | ZA (v) | Mediator of RNA polymerase II transcription subunit 10 | polymer | 135 | 15711.0 | 1 | UniProt (Q9BTT4) Pfam (PF09748) | Homo sapiens (Human) | Mediator complex subunit 10,Transformation-related gene 17 protein,TRG-17,Transformation-related gene 20 protein,TRG-20 |
| 53 | AB (w) | Mediator of RNA polymerase II transcription subunit 19 | polymer | 244 | 26321.1 | 1 | UniProt (A0JLT2) Pfam (PF10278) | Homo sapiens (Human) | Lung cancer metastasis-related protein 1,Mediator complex subunit 19 |
| 54 | BB (x) | Mediator of RNA polymerase II transcription subunit 21 | polymer | 144 | 15575.2 | 1 | UniProt (Q13503) Pfam (PF11221) | Homo sapiens (Human) | Mediator complex subunit 21,RNA polymerase II holoenzyme component SRB7,RNAPII complex component SRB7,hSrb7 |
| 55 | CB (y) | Mediator of RNA polymerase II transcription subunit 31 | polymer | 131 | 15826.1 | 1 | UniProt (Q9Y3C7) Pfam (PF05669) | Homo sapiens (Human) | Mediator complex subunit 31,Mediator complex subunit SOH1,hSOH1 |
| 56 | DB (z) | Mediator of RNA polymerase II transcription subunit 15 | polymer | 788 | 86830.1 | 1 | UniProt (Q96RN5) Pfam (PF09606) Pfam (PF21538) Pfam (PF21539) | Homo sapiens (Human) | Activator-recruited cofactor 105 kDa component,ARC105,CTG repeat protein 7a,Mediator complex subunit 15,Positive cofactor 2 glutamine/Q-rich-associated protein,PC2 glutamine/Q-rich-associated protein,TPA-inducible gene 1 protein,TIG-1,Trinucleotide repeat-containing gene 7 protein |
| 57 | EB, HB (A) | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) | |||
| 58 | FB, GB, IB, JB, KB... (A, B, C, I, J...) | ZINC ION | non-polymer | 65.4 | 16 | Chemie (ZN) | |||
| 59 | QB (X) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 1 | Chemie (SF4) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 56 |
| Total formula weight | 2507797.6 | |
| Non-Polymers* | Number of molecules | 19 |
| Total formula weight | 1446.8 | |
| All* | Total formula weight | 2509244.4 |
