IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA (> 100) / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit RPB4 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA (> 100) / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit RPB4 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 24 / Mediator of RNA polymerase II transcription subunit 6 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB1 / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB2 / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / DNA-directed RNA polymerase II subunit RPB9 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription initiation factor IIB / Mediator of RNA polymerase II transcription subunit 21 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 27 / General transcription factor IIH subunit 5 / Mediator of RNA polymerase II transcription subunit 25 / General transcription factor IIH subunit 4 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 15 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 29 / Mediator of RNA polymerase II transcription subunit 11 / Mediator of RNA polymerase II transcription subunit 23 / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 31 Similarity search - Component
Biological species
Homo sapiens (human)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
National Institutes of Health/National Cancer Institute (NIH/NCI)
P01-CA092584
United States
National Institutes of Health/National Cancer Institute (NIH/NCI)
U54-CA193419
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
T32-GM008382
United States
Citation
Journal: Science / Year: 2021 Title: Structure of the human Mediator-bound transcription preinitiation complex. Authors: R Abdella / A Talyzina / S Chen / C J Inouye / R Tjian / Y He / Abstract: Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is ...Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.
Mass: 93136.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9Y2X0
Mass: 49516.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083
#34: Protein
CDK-activatingkinaseassemblyfactorMAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36
Mass: 35873.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51948
Mass: 110430.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: O75448
Mass: 78230.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q71SY5
Mass: 28464.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: O75586
Mass: 29112.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q96G25
Mass: 13145.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9P086
Mass: 72984.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9NVC6
Mass: 23693.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9BUE0
Mass: 23243.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9H944
#43: Protein
MediatorofRNApolymeraseIItranscriptionsubunit22 / Mediator complex subunit 22 / Surfeit locus protein 5 / Surf-5
Mass: 22243.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q15528
Mass: 35478.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q6P2C8
#45: Protein
MediatorofRNApolymeraseIItranscriptionsubunit28 / Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting ...Endothelial-derived protein 1 / Mediator complex subunit 28 / Merlin and Grb2-interacting cytoskeletal protein / Magicin / Tumor angiogenesis marker EG-1
Mass: 19540.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9H204
#46: Protein
MediatorofRNApolymeraseIItranscriptionsubunit29 / Intersex-like protein / Mediator complex subunit 29
Mass: 21089.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9NX70
Mass: 20301.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q96HR3
Mass: 160787.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: O60244
Mass: 29781.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9NPJ6
Mass: 16422.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9NWA0
Mass: 15710.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9BTT4
#53: Protein
MediatorofRNApolymeraseIItranscriptionsubunit19 / Lung cancer metastasis-related protein 1 / Mediator complex subunit 19
Mass: 26321.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: A0JLT2
Mass: 15826.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q9Y3C7
#56: Protein
MediatorofRNApolymeraseIItranscriptionsubunit15 / Activator-recruited cofactor 105 kDa component / ARC105 / CTG repeat protein 7a / Mediator complex ...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
Mass: 86830.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q96RN5
DNA-directedRNApolymeraseIIsubunitRPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...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
Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P24928, DNA-directed RNA polymerase
#6: Protein
DNA-directedRNApolymeraseIIsubunitRPB2 / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA ...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
Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P30876, DNA-directed RNA polymerase
#7: Protein
DNA-directedRNApolymeraseIIsubunitRPB3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA- ...RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31
Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P19387
#8: Protein
DNA-directedRNApolymeraseIIsubunitRPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa ...RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16
Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: O15514
#9: Protein
DNA-directedRNApolymeraseIIsubunitRPB5 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA DNA-directed RNA polymerases I / ...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
Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P19388
#11: Protein
DNA-directedRNApolymeraseIIsubunitRPB7 / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa ...RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19
Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62487
#13: Protein
DNA-directedRNApolymeraseIIsubunitRPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5
Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P36954
#15: Protein
DNA-directedRNApolymeraseIIsubunitRPB11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit
Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P52435
+
DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules FHJL
#10: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...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
Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P61218
#12: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...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
Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P52434
#14: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...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
Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P62875
#16: Protein
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...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
Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P53803
Mass: 28427.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2F2, RAP30 / Production host: Escherichia coli (E. coli) / References: UniProt: P13984, DNA helicase
+
Super core promoter ... , 2 types, 2 molecules UV
#25: DNA chain
supercorepromotersensestrand
Mass: 31002.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#26: DNA chain
supercorepromoterantisensestrand
Mass: 30708.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
TFIIHbasaltranscriptionfactorcomplexhelicaseXPBsubunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...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
Mass: 89404.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P19447, DNA helicase
#28: Protein
TFIIHbasaltranscriptionfactorcomplexhelicaseXPDsubunit / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 ...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
Mass: 87021.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P18074, DNA helicase
Mass: 62116.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: P32780
Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q92759
Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q13888
Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q13889
Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA / References: UniProt: Q6ZYL4
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