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- PDB-7nvr: Human Mediator with RNA Polymerase II Pre-initiation complex -

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Basic information

Entry
Database: PDB / ID: 7nvr
TitleHuman Mediator with RNA Polymerase II Pre-initiation complex
Components
  • (DNA-directed RNA polymerase ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 2
  • (General transcription ...) x 9
  • (Mediator of RNA polymerase II transcription subunit ...) x 18
  • (Transcription initiation factor ...) x 4
  • (Unassigned peptide, likely ...) x 2
  • (unassigned peptide ...) x 6
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
  • NT
  • RNA polymerase II subunit K
  • RNA_pol_L_2 domain-containing protein
  • RPOL4c domain-containing protein
  • TATA-box-binding protein
  • TEMPLATE
  • TFIIH basal transcription factor complex helicase XPD subunit
KeywordsTRANSCRIPTION / Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / cyclin-dependent protein kinase activating kinase holoenzyme complex / core mediator complex / MMXD complex / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / core TFIIH complex portion of holo TFIIH complex ...negative regulation of smooth muscle cell differentiation / cyclin-dependent protein kinase activating kinase holoenzyme complex / core mediator complex / MMXD complex / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / B-WICH complex positively regulates rRNA expression / transcription factor TFIIK complex / positive regulation of mitotic recombination / RNA polymerase II core complex assembly / Transcriptional regulation by small RNAs / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Pol II CTD phosphorylation and interaction with CE / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / adult heart development / hair cell differentiation / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleotide-excision repair factor 3 complex / embryonic cleavage / transcription factor TFIIE complex / phosphatase activator activity / TFIIF-class transcription factor complex binding / negative regulation of DNA helicase activity / [RNA-polymerase]-subunit kinase / positive regulation of core promoter binding / transcription factor TFIIH core complex / UV protection / transcription factor TFIIH holo complex / transcription factor TFIIF complex / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / transcription elongation from RNA polymerase I promoter / G protein-coupled receptor internalization / RNA Polymerase III Transcription Initiation From Type 3 Promoter / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase III Abortive And Retractive Initiation / phosphorylation of RNA polymerase II C-terminal domain / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / Abortive elongation of HIV-1 transcript in the absence of Tat / limb development / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / 5'-3' DNA helicase activity / RNA polymerase II general transcription initiation factor binding / nuclear-transcribed mRNA catabolic process, exonucleolytic / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / FGFR2 alternative splicing / Generic Transcription Pathway / male pronucleus / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / female pronucleus / Viral Messenger RNA Synthesis / mRNA Capping / mediator complex / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / 3'-5' DNA helicase activity / positive regulation of viral transcription / mRNA export from nucleus in response to heat stress / transcription initiation from RNA polymerase I promoter / bone mineralization / thyroid hormone receptor binding / RNA polymerase II preinitiation complex assembly / vitamin D receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / Processing of Capped Intron-Containing Pre-mRNA / cortical actin cytoskeleton / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation
Similarity search - Function
Mediator complex subunit 28 / Mediator complex subunit 30 / Mediator complex, subunit Med30, metazoa / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med19, metazoa / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator complex, subunit Med28 / Mediator complex, subunit Med27 / Mediator complex subunit 27 ...Mediator complex subunit 28 / Mediator complex subunit 30 / Mediator complex, subunit Med30, metazoa / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med19, metazoa / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator complex, subunit Med28 / Mediator complex, subunit Med27 / Mediator complex subunit 27 / Transcription factor subunit Med10 of Mediator complex / Mediator complex, subunit Med10 / RNA polymerase II transcription mediator complex subunit 9 / Mediator of RNA polymerase II transcription subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Subunit 21 of Mediator complex / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Mediator complex protein / CyclinH/Ccl1 / Mediator complex, subunit Med11 / Cyclin-dependent kinase 7 / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Cyclin C-terminal domain / Cyclin, C-terminal domain 2 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med20 / Subunit 17 of Mediator complex / MED6 mediator sub complex component / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / : / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator of RNA polymerase II transcription subunit 22 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator complex, subunit Med8, fungi/metazoa / Med18 protein / Mediator complex, subunit Med18 / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / CDK-activating kinase assembly factor MAT1 / C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE alpha subunit, C-terminal / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / RAD3/XPD family / Ssl1-like / TFIIH subunit Tfb1/GTF2H1 / Ssl1-like / TFIIH subunit Ssl1/p44 / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / BSD domain profile. / BSD domain / BSD domain / domain in transcription factors and synapse-associated proteins / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / Helicase XPB/Ssl2 / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 (p52) C-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH complex subunit Tfb5 / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / DEAD2 / Helicase-like, DEXD box c2 type / Helicase C-terminal domain / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / ATP-dependent helicase, C-terminal / HELICc2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIE beta central core DNA-binding domain profile. / TFIIE beta subunit core domain / Transcription initiation factor TFIIE, beta subunit / TFA2 Winged helix domain 2 / TFA2, Winged helix domain 2 / Cyclin/Cyclin-like subunit Ssn8
Similarity search - Domain/homology
Cyclin-H / CDK-activating kinase assembly factor MAT1 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / 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 ...Cyclin-H / CDK-activating kinase assembly factor MAT1 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / 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 4 / General transcription factor IIH subunit 5 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / 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 11 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / General transcription factor IIF subunit 1 / Cyclin-dependent kinase 7 / IRON/SULFUR CLUSTER / General transcription factor IIH subunit 1 / DNA-directed RNA polymerase II subunit RPB3 / : / DNA / DNA (> 10) / DNA (> 100) / RNA polymerase II subunit D / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerase subunit beta / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit K / DNA-directed RNA polymerase II subunit E / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 6 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / TATA-box-binding protein / General transcription factor IIE subunit 1 / Mediator of RNA polymerase II transcription subunit 31
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
Trichoplusia ni (cabbage looper)
Human mastadenovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRengachari, S. / Schilbach, S. / Aibara, S. / Cramer, P.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357European Union
H2020 Marie Curie Actions of the European Commission894862European Union
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 16, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
0: TFIIH basal transcription factor complex helicase XPD subunit
1: General transcription factor IIH subunit 1
2: General transcription factor IIH subunit 4
3: CDK-activating kinase assembly factor MAT1
4: General transcription factor IIH subunit 3
5: General transcription factor IIH subunit 5
6: General transcription factor IIH subunit 2
7: General transcription and DNA repair factor IIH helicase subunit XPB
8: Cyclin-dependent kinase 7
9: Cyclin-H
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RPOL4c domain-containing protein
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerase II subunit F
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: RNA_pol_L_2 domain-containing protein
L: RNA polymerase II subunit K
M: Transcription initiation factor IIB
N: NT
O: TATA-box-binding protein
Q: General transcription factor IIF subunit 1
R: General transcription factor IIF subunit 2
T: TEMPLATE
U: Transcription initiation factor IIA subunit 1
V: Transcription initiation factor IIA subunit 2
W: General transcription factor IIE subunit 1
X: Transcription initiation factor IIE subunit beta
Y: Unassigned peptide, likely TFIIE-beta
Z: Unassigned peptide, likely XPB
a: Mediator of RNA polymerase II transcription subunit 6
b: Mediator of RNA polymerase II transcription subunit 8
c: Mediator of RNA polymerase II transcription subunit 11
d: Mediator of RNA polymerase II transcription subunit 17
e: Mediator of RNA polymerase II transcription subunit 18
f: Mediator of RNA polymerase II transcription subunit 20
g: Mediator of RNA polymerase II transcription subunit 22
h: Mediator of RNA polymerase II transcription subunit 4
i: Mediator of RNA polymerase II transcription subunit 7
j: Mediator of RNA polymerase II transcription subunit 9
k: Mediator of RNA polymerase II transcription subunit 10
l: Mediator of RNA polymerase II transcription subunit 14
m: Mediator of RNA polymerase II transcription subunit 19
n: Mediator of RNA polymerase II transcription subunit 21
o: Mediator of RNA polymerase II transcription subunit 31
p: Mediator of RNA polymerase II transcription subunit 27
q: Mediator of RNA polymerase II transcription subunit 28
r: unassigned peptide (MED29 or MED30)
s: Mediator of RNA polymerase II transcription subunit 30
v: unassigned peptide (MED14)
w: unassigned peptide (MED6)
x: unassigned peptide (MED17)
y: unassigned peptide (MED29 or MED30)
z: unassigned peptide (MED29 or MED30)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,978,50278
Polymers1,976,94958
Non-polymers1,55320
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 8 molecules 0389DKLO

#1: Protein TFIIH basal transcription factor complex helicase XPD subunit / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18074, DNA helicase
#4: Protein CDK-activating kinase assembly factor MAT1 / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51948
#9: Protein Cyclin-dependent kinase 7 / / 39 kDa protein kinase / p39 Mo15 / CDK-activating kinase 1 / Cell division protein kinase 7 / ...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


Mass: 39090.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#10: Protein Cyclin-H / MO15-associated protein / p34 / p37


Mass: 37695.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51946
#14: Protein RPOL4c domain-containing protein


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4
#21: Protein RNA_pol_L_2 domain-containing protein


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25
#22: Protein RNA polymerase II subunit K /


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51
#25: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20226

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General transcription ... , 9 types, 9 molecules 124567QRW

#2: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 62116.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32780
#3: Protein General transcription factor IIH subunit 4 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13889
#6: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZYL4
#7: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44481.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13888
#8: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair ...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


Mass: 89404.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19447, DNA helicase
#26: Protein General transcription factor IIF subunit 1 / General transcription factor IIF 74 kDa subunit / Transcription initiation factor IIF subunit alpha ...General transcription factor IIF 74 kDa subunit / Transcription initiation factor IIF subunit alpha / TFIIF-alpha / Transcription initiation factor RAP74


Mass: 58343.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2F1, RAP74 / Production host: Escherichia coli (E. coli) / References: UniProt: P35269
#27: Protein General transcription factor IIF subunit 2 / ATP-dependent helicase GTF2F2 / General transcription factor IIF 30 kDa subunit / Transcription ...ATP-dependent helicase GTF2F2 / General transcription factor IIF 30 kDa subunit / Transcription initiation factor IIF subunit beta / TFIIF-beta / Transcription initiation factor RAP30


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
#31: Protein General transcription factor IIE subunit 1 / General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha ...General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha / TFIIE-alpha


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

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DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCEFGI

#11: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#15: Protein DNA-directed RNA polymerase II subunit E / Polymerase / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7
#16: Protein DNA-directed RNA polymerase II subunit F / Polymerase / DNA-directed RNA polymerases I / II / and III subunit RPABC2 / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8
#17: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJZ9
#19: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / 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) Sus scrofa (pig) / References: UniProt: P60899

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ

#18: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULF2
#20: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0

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Transcription initiation factor ... , 4 types, 4 molecules MUVX

#23: Protein Transcription initiation factor IIB / General transcription factor TFIIB / S300-II


Mass: 34877.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403, histone acetyltransferase
#29: Protein Transcription initiation factor IIA subunit 1 / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa ...General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42


Mass: 41544.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655
#30: Protein Transcription initiation factor IIA subunit 2 / General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIA-12 / TFIIAS / Transcription ...General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIA-12 / TFIIAS / Transcription initiation factor IIA gamma chain / TFIIA-gamma


Mass: 12469.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657
#32: Protein Transcription initiation factor IIE subunit beta / TFIIE-beta / General transcription factor IIE subunit 2


Mass: 33106.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E2, TF2E2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29084

+
DNA chain , 2 types, 2 molecules NT

#24: DNA chain NT


Mass: 32911.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521
#28: DNA chain TEMPLATE


Mass: 32508.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521

+
Unassigned peptide, likely ... , 2 types, 2 molecules YZ

#33: Protein/peptide Unassigned peptide, likely TFIIE-beta


Mass: 1635.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#34: Protein/peptide Unassigned peptide, likely XPB


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

+
Mediator of RNA polymerase II transcription subunit ... , 18 types, 18 molecules abcdefghijklmnopqs

#35: Protein Mediator of RNA polymerase II transcription subunit 6 / Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal ...Activator-recruited cofactor 33 kDa component / ARC33 / Mediator complex subunit 6 / hMed6 / Renal carcinoma antigen NY-REN-28


Mass: 28464.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED6, ARC33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75586
#36: Protein Mediator of RNA polymerase II transcription subunit 8 / Activator-recruited cofactor 32 kDa component / ARC32 / Mediator complex subunit 8


Mass: 29112.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96G25
#37: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 13145.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED11, HSPC296 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9P086
#38: Protein Mediator of RNA polymerase II transcription subunit 17 / Activator-recruited cofactor 77 kDa component / ARC77 / Cofactor required for Sp1 transcriptional ...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


Mass: 72984.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED17, ARC77, CRSP6, DRIP77, DRIP80, TRAP80 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVC6
#39: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / p28b


Mass: 23693.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED18 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BUE0
#40: Protein Mediator of RNA polymerase II transcription subunit 20 / Mediator complex subunit 20 / TRF-proximal protein homolog / hTRFP


Mass: 23243.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED20, TRFP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H944
#41: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Surfeit locus protein 5 / Surf-5


Mass: 22243.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED22, SURF5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15528
#42: Protein Mediator of RNA polymerase II transcription subunit 4 / Activator-recruited cofactor 36 kDa component / ARC36 / Mediator complex subunit 4 / TRAP/SMCC/PC2 ...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


Mass: 29781.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED4, ARC36, DRIP36, VDRIP, HSPC126 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NPJ6
#43: Protein Mediator of RNA polymerase II transcription subunit 7 / hMED7 / Activator-recruited cofactor 34 kDa component / ARC34 / Cofactor required for Sp1 ...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


Mass: 27285.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED7, ARC34, CRSP9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O43513
#44: Protein Mediator of RNA polymerase II transcription subunit 9 / Mediator complex subunit 9


Mass: 16422.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED9, MED25 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NWA0
#45: Protein Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation- ...Mediator complex subunit 10 / Transformation-related gene 17 protein / TRG-17 / Transformation-related gene 20 protein / TRG-20


Mass: 15710.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED10, L6, TRG17, TRG20 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BTT4
#46: Protein Mediator of RNA polymerase II transcription subunit 14 / Activator-recruited cofactor 150 kDa component / ARC150 / Cofactor required for Sp1 transcriptional ...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


Mass: 160787.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: MED14, ARC150, CRSP2, CXorf4, DRIP150, EXLM1, RGR1, TRAP170
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60244
#47: Protein Mediator of RNA polymerase II transcription subunit 19 / Lung cancer metastasis-related protein 1 / Mediator complex subunit 19


Mass: 26321.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED19, LCMR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0JLT2
#48: Protein Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex ...Mediator complex subunit 21 / RNA polymerase II holoenzyme component SRB7 / RNAPII complex component SRB7 / hSrb7


Mass: 15575.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED21, SRB7, SURB7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13503
#49: Protein Mediator of RNA polymerase II transcription subunit 31 / Mediator complex subunit 31 / Mediator complex subunit SOH1 / hSOH1


Mass: 15826.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED31, SOH1, CGI-125 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y3C7
#50: Protein Mediator of RNA polymerase II transcription subunit 27 / Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator ...Cofactor required for Sp1 transcriptional activation subunit 8 / CRSP complex subunit 8 / Mediator complex subunit 27 / P37 TRAP/SMCC/PC2 subunit / Transcriptional coactivator CRSP34


Mass: 35478.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED27, CRSP34, CRSP8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P2C8
#51: Protein Mediator of RNA polymerase II transcription subunit 28 / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED28, EG1, FKSG20 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H204
#53: Protein Mediator of RNA polymerase II transcription subunit 30 / Mediator complex subunit 30 / TRAP/Mediator complex component TRAP25 / Thyroid hormone receptor- ...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


Mass: 20301.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MED30, THRAP6, TRAP25 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96HR3

+
Unassigned peptide ... , 6 types, 6 molecules rvwxyz

#52: Protein/peptide unassigned peptide (MED29 or MED30)


Mass: 1720.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#54: Protein/peptide unassigned peptide (MED14)


Mass: 1890.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#55: Protein/peptide unassigned peptide (MED6)


Mass: 1379.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#56: Protein/peptide unassigned peptide (MED17)


Mass: 954.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#57: Protein/peptide unassigned peptide (MED29 or MED30)


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)
#58: Protein/peptide unassigned peptide (MED29 or MED30)


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)

+
Non-polymers , 3 types, 20 molecules

#59: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#60: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human Mediator with RNA Polymerase II Pre-initiation complexCOMPLEX#1-#580MULTIPLE SOURCES
2Pol Complex and Mediator of RNA polymerase II transcriptionCOMPLEX#1-#10, #25, #34-#561RECOMBINANT
3DNA-directed RNA polymerasePolymeraseCOMPLEX#11-#221NATURAL
4NT and TemplateCOMPLEX#24, #281RECOMBINANT
5unassigned peptides (MED29 or MED30)COMPLEX#57-#581NATURAL
6Transcription initiation factorsCOMPLEX#23, #26-#27, #29-#331RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Sus scrofa (pig)9823
34Human mastadenovirus C129951
45Trichoplusia ni (cabbage looper)7111
56Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
24synthetic construct (others)32630
36Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 58.56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25967 / Symmetry type: POINT

+
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