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- PDB-7nvy: RNA polymerase II pre-initiation complex with closed promoter DNA... -

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Entry
Database: PDB / ID: 7nvy
TitleRNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 2
  • (General transcription ...) x 9
  • (Transcription initiation factor ...) x 4
  • (Unassigned peptide, likely ...) x 2
  • CDK-activating kinase assembly factor MAT1
  • DNA-directed RNA polymerase subunit betaPolymerase
  • Non-template DNA
  • RNA polymerase II subunit K
  • RNA_pol_L_2 domain-containing protein
  • RPB1POLR2A
  • RPOL4c domain-containing protein
  • TATA-box-binding protein
  • TFIIH basal transcription factor complex helicase XPD subunit
  • Template DNA
KeywordsTRANSCRIPTION / Initiation
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / B-WICH complex positively regulates rRNA expression ...RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / B-WICH complex positively regulates rRNA expression / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination / transcription factor TFIIK complex / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / Processing of Capped Intron-Containing Pre-mRNA / TP53 Regulates Transcription of DNA Repair Genes / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / mRNA Splicing - Minor Pathway / mRNA Splicing - Major Pathway / mRNA Capping / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / Estrogen-dependent gene expression / RNA Polymerase II Transcription Elongation / FGFR2 alternative splicing / RNA Polymerase II Transcription Initiation / RNA Pol II CTD phosphorylation and interaction with CE / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / Formation of TC-NER Pre-Incision Complex / RNA polymerase II core complex assembly / adult heart development / hair cell differentiation / 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 / transcription factor TFIIH core complex / positive regulation of core promoter binding / transcription factor TFIIH holo complex / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / G protein-coupled receptor internalization / transcription elongation from RNA polymerase I promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / phosphorylation of RNA polymerase II C-terminal domain / RNA Polymerase III Abortive And Retractive Initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription factor TFIIA complex / 5'-3' DNA helicase activity / RNA polymerase III general transcription initiation factor activity / nuclear-transcribed mRNA catabolic process, exonucleolytic / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / FGFR2 alternative splicing / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / mRNA export from nucleus in response to heat stress / 3'-5' DNA helicase activity / positive regulation of viral transcription / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / bone mineralization / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Transcription Initiation And Promoter Clearance / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Transcription Initiation / Transcription of the HIV genome / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / termination of RNA polymerase I transcription
Similarity search - Function
CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / Zinc finger, C3HC4 type (RING finger) / TFIIH subunit Tfb1/GTF2H1 / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFIIH p62 subunit, N-terminal domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb4/GTF2H3 ...CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / Zinc finger, C3HC4 type (RING finger) / TFIIH subunit Tfb1/GTF2H1 / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFIIH p62 subunit, N-terminal domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / BSD domain profile. / Ssl1-like / domain in transcription factors and synapse-associated proteins / TFIIH C1-like domain / TFIIH subunit Ssl1/p44 / BSD domain / Ssl1-like / TFIIH C1-like domain / BSD domain / RAD3/XPD family / TFIIH C1-like domain / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase conserved C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase XPB/Ssl2 / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2, C-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / DEAD2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEAD_2 / Helicase-like, DEXD box c2 type / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEXDc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / HELICc2 / Transcription initiation factor TFIIE, beta subunit / TFIIE beta central core DNA-binding domain profile. / TFIIE beta subunit core domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFA2 Winged helix domain 2 / TFA2, Winged helix domain 2 / TFIIE alpha subunit / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E / Transcription initiation factor IIE / Transcription initiation factor IIE subunit alpha, N-terminal / TFE/IIEalpha-type HTH domain profile. / TFIIEalpha/SarR/Rpc3 HTH domain / TFIIF, beta subunit N-terminus / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / Type III restriction enzyme, res subunit / Helicase/UvrB, N-terminal / Transcription factor TFIID repeat signature. / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein / TATA-box binding protein, conserved site / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily
Similarity search - Domain/homology
CDK-activating kinase assembly factor MAT1 / TATA-box-binding protein / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / Transcription initiation factor IIB / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 ...CDK-activating kinase assembly factor MAT1 / TATA-box-binding protein / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / Transcription initiation factor IIB / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / General transcription factor IIH subunit 5 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPB / IRON/SULFUR CLUSTER / General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit E / RNA polymerase II subunit K / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / RNA polymerase II subunit D / DNA (> 100) / DNA (> 10) / DNA / : / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
Human mastadenovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsAibara, S. / Schilbach, S. / Cramer, P.
Funding support Germany, 5items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
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)882357 Germany
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 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
A: RPB1
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: Non-template DNA
O: TATA-box-binding protein
Q: General transcription factor IIF subunit 1
R: General transcription factor IIF subunit 2
T: Template DNA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,296,26251
Polymers1,294,77432
Non-polymers1,48819
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area144930 Å2
ΔGint-804 kcal/mol
Surface area348310 Å2
MethodPISA

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Components

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Protein , 8 types, 8 molecules 03ABDKLO

#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 RPB1 / POLR2A


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#10: 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
#12: 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
#19: 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
#20: 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
#23: 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
#24: 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
#25: 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
#29: 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 II subunit ... , 5 types, 5 molecules CEFGI

#11: 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
#13: 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
#14: 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
#15: 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
#17: 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

#16: 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
#18: 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

#21: 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
#27: 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
#28: 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
#30: 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

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DNA chain , 2 types, 2 molecules NT

#22: DNA chain Non-template DNA


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


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

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

#31: 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)
#32: 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)

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Non-polymers , 3 types, 19 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#35: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
Type: COMPLEX / Entity ID: #1-#32 / Source: MULTIPLE SOURCES
Molecular weightValue: 1.37 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 41.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15226 / Symmetry type: POINT

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