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- PDB-30ff: TFIID-containing RNA polymerase II pre-initiation complex in the ... -

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Entry
Database: PDB / ID: 30ff
TitleTFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosome
Components
  • (DNA-directed RNA polymerase ...) x 6
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 4
  • (General transcription ...) x 9
  • (RNA polymerase II subunit ...) x 2
  • (Transcription initiation factor ...) x 17
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Non-template DNA
  • TATA-box-binding protein
  • TFIIH basal transcription factor complex helicase XPD subunit
  • Template DNA
KeywordsTRANSCRIPTION / Mammalian PIC / +1 nucleosome / transcription initiation
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation ...RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Regulation of TP53 Activity through Phosphorylation / negative regulation of MHC class I biosynthetic process / response to paraquat / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex / positive regulation of androgen receptor signaling pathway / MMXD complex / TFIIH-class transcription factor complex binding / core TFIIH complex portion of holo TFIIH complex / histone H3K27me3 reader activity / negative regulation of protein autoubiquitination / positive regulation of core promoter binding / negative regulation of MHC class II biosynthetic process / Cytosolic iron-sulfur cluster assembly / transcription factor TFTC complex / RNA polymerase II core complex assembly / central nervous system myelin formation / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of mitotic recombination / transcription factor TFIIE complex / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / hair cell differentiation / SLIK (SAGA-like) complex / nucleotide-excision repair factor 3 complex / phosphatase activator activity / nucleotide-excision repair, preincision complex assembly / snRNA transcription by RNA polymerase II / Regulation of TP53 Activity through Phosphorylation / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / hair follicle maturation / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIK complex / RNA polymerase I core promoter sequence-specific DNA binding / CAK-ERCC2 complex / embryonic cleavage / transcription factor TFIIF complex / positive regulation of response to cytokine stimulus / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / mRNA Polyadenylation / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / C2H2 zinc finger domain binding / UV protection / maintenance of protein location in nucleus / RNA Polymerase III Abortive And Retractive Initiation / regulation of cyclin-dependent protein serine/threonine kinase activity / male pronucleus / female pronucleus / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / host-mediated activation of viral transcription
Similarity search - Function
TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / : / : / TAFII55 protein conserved region / TAF2 Ig-like domain / TAF2-like, TPR repeats ...TAFII28-like protein domain / Transcription initiation factor TFIID subunit 11-like / hTAFII28-like protein conserved region / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / : / : / TAFII55 protein conserved region / TAF2 Ig-like domain / TAF2-like, TPR repeats / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor TFIID component TAF4, C-terminal / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / Transcription initiation factor IID, subunit 13 / : / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, 31kD subunit / Bromodomain transcription factors and PHD domain containing proteins / Transcription initiation factor TAFII31 / Bromodomain associated / Bromodomain associated domain / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TATA box binding protein associated factor (TAF) / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 12 domain / TAF6, C-terminal HEAT repeat domain / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / : / MAT1 C-terminal CAK anchor / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / : / Transcription initiation factor IIE subunit alpha, N-terminal
Similarity search - Domain/homology
(2S)-2-aminopropan-1-ol / ALANINE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA (> 100) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...(2S)-2-aminopropan-1-ol / ALANINE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA (> 100) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase II subunit J / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / Transcription initiation factor TFIID subunit 4 / Histone H2B 1.1 / Histone H2A type 1 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / TATA-box-binding protein / Transcription initiation factor TFIID subunit 1 / 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 TFIID subunit 6 / Cyclin-dependent kinase 7 / 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 / Histone H4 / Histone H3.2 / Transcription initiation factor IIB / Transcription initiation factor TFIID subunit 10 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / General transcription factor IIH subunit 5 / Transcription initiation factor TFIID subunit 8 / Transcription initiation factor TFIID subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Sus scrofa (pig)
unidentified adenovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsZhan, Y. / Abril-Garrido, J. / Grabbe, F. / Seweryn, P. / Neef, U. / Dienemann, C. / Cramer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published / Year: 2026
Title: RNA polymerase II elongation complex with the +1 nucleosome
Authors: Zhan, Y. / Abril-Garrido, J.
History
DepositionApr 22, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: General transcription and DNA repair factor IIH helicase subunit XPB
1: TFIIH basal transcription factor complex helicase XPD subunit
2: General transcription factor IIH subunit 1
3: General transcription factor IIH subunit 4
4: General transcription factor IIH subunit 2
5: General transcription factor IIH subunit 3
6: General transcription factor IIH subunit 5
7: CDK-activating kinase assembly factor MAT1
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: DNA-directed RNA polymerase II subunit RPB4
DA: Transcription initiation factor TFIID subunit 1
DB: Transcription initiation factor TFIID subunit 2
DD: Transcription initiation factor TFIID subunit 4
DE: Transcription initiation factor TFIID subunit 5
DF: Transcription initiation factor TFIID subunit 6
DG: Transcription initiation factor TFIID subunit 7
DH: Transcription initiation factor TFIID subunit 8
DI: Transcription initiation factor TFIID subunit 9
DJ: Transcription initiation factor TFIID subunit 10
DL: Transcription initiation factor TFIID subunit 12
Dc: Transcription initiation factor TFIID subunit 3
Dd: Transcription initiation factor TFIID subunit 4
De: Transcription initiation factor TFIID subunit 5
Df: Transcription initiation factor TFIID subunit 6
Di: Transcription initiation factor TFIID subunit 9
Dj: Transcription initiation factor TFIID subunit 10
Dk: Transcription initiation factor TFIID subunit 11
Dl: Transcription initiation factor TFIID subunit 12
Dm: Transcription initiation factor TFIID subunit 13
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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 polymerase II subunit J
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
a: Histone H3.2
b: Histone H4
c: Histone H2A type 1
d: Histone H2B 1.1
e: Histone H3.2
f: Histone H4
g: Histone H2A type 1
h: Histone H2B 1.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,822,649105
Polymers2,819,09159
Non-polymers3,55846
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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General transcription ... , 9 types, 9 molecules 023456QRW

#1: 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
#3: 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
#4: 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 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
#6: 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
#7: 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
#39: 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
#40: 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
#44: 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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Protein , 9 types, 13 molecules 1789Oaebfcgdh

#2: 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
#8: 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
#38: 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
#46: Protein Histone H3.2


Mass: 15421.101 Da / Num. of mol.: 2 / Mutation: G103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#47: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#48: Protein Histone H2A type 1


Mass: 14093.436 Da / Num. of mol.: 2 / Mutation: G100R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#49: Protein Histone H2B 1.1 / H2B1.1


Mass: 13965.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA-directed RNA polymerase ... , 6 types, 6 molecules ABCDGI

#11: Protein DNA-directed RNA polymerase subunit


Mass: 218889.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A7M4DUC2, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerase subunit beta


Mass: 147938.594 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


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#14: Protein DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit rpb4


Mass: 20962.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4
#30: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7
#32: Protein DNA-directed RNA polymerase II subunit RPB9 / 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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Transcription initiation factor ... , 17 types, 23 molecules DADBDDDdDEDeDFDfDGDHDIDiDJDjDLDlDcDkDmMUVX

#15: Protein Transcription initiation factor TFIID subunit 1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor ...Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor TFIID 250 kDa subunit / TAF(II)250 / TAFII-250 / TAFII250


Mass: 214992.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#16: Protein Transcription initiation factor TFIID subunit 2 / 150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP- ...150 kDa cofactor of initiator function / RNA polymerase II TBP-associated factor subunit B / TBP-associated factor 150 kDa / Transcription initiation factor TFIID 150 kDa subunit / TAF(II)150 / TAFII-150 / TAFII150


Mass: 137159.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF2, CIF150, TAF2B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1X5
#17: Protein Transcription initiation factor TFIID subunit 4 / RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription ...RNA polymerase II TBP-associated factor subunit C / TBP-associated factor 4 / Transcription initiation factor TFIID 130 kDa subunit / TAF(II)130 / TAFII-130 / TAFII130 / Transcription initiation factor TFIID 135 kDa subunit / TAF(II)135 / TAFII-135 / TAFII135


Mass: 110221.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF4, TAF2C, TAF2C1, TAF4A, TAFII130, TAFII135 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00268
#18: Protein Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID 100 kDa subunit / TAF(II)100 / TAFII-100 / TAFII100


Mass: 86932.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Taf5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8C092
#19: Protein Transcription initiation factor TFIID subunit 6 / RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa ...RNA polymerase II TBP-associated factor subunit E / Transcription initiation factor TFIID 70 kDa subunit / TAF(II)70 / TAFII-70 / TAFII70 / Transcription initiation factor TFIID 80 kDa subunit / TAF(II)80 / TAFII-80 / TAFII80


Mass: 72749.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF6, TAF2E, TAFII70 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49848
#20: Protein Transcription initiation factor TFIID subunit 7


Mass: 40325.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, QccE-10107 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4R5A5
#21: Protein Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription ...Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / TAFII-43 / TAFII43 / hTAFII43


Mass: 34304.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF8, TAFII43, TBN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7Z7C8
#22: Protein Transcription initiation factor TFIID subunit 9


Mass: 29006.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q17QQ4
#23: Protein Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAF(II)30 / TAFII-30 / TAFII30


Mass: 21731.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF10, TAF2A, TAF2H, TAFII30 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12962
#24: Protein Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID 20/15 kDa subunits / TAFII-20/TAFII-15 / TAFII20/TAFII15


Mass: 17948.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF12, TAF15, TAF2J, TAFII20 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16514
#25: Protein Transcription initiation factor TFIID subunit 3


Mass: 103769.320 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)
#26: Protein Transcription initiation factor TFIID subunit 11 / TFIID subunit p30-beta / Transcription initiation factor TFIID 28 kDa subunit / TAF(II)28 / TAFII-28 / TAFII28


Mass: 23340.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF11, TAF2I, PRO2134 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15544
#27: Protein Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID 18 kDa subunit / TAF(II)18 / TAFII-18 / TAFII18


Mass: 14307.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q148M7
#36: 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
#42: 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: Trichoplusia ni (cabbage looper) / References: UniProt: P52655
#43: 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: Trichoplusia ni (cabbage looper) / References: UniProt: P52657
#45: 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-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules EFHJ

#28: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VTX4
#29: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit F / RPB6 homolog


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VEK9
#31: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2
#33: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit L


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8W4F9W9

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RNA polymerase II subunit ... , 2 types, 2 molecules KL

#34: Protein RNA polymerase II subunit J


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0TE17
#35: 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: A0A8D0JYF1

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DNA chain , 2 types, 2 molecules NT

#37: DNA chain Non-template DNA


Mass: 70013.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus
#41: DNA chain Template DNA


Mass: 70177.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus

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Non-polymers , 5 types, 46 molecules

#50: Chemical...
ChemComp-2A1 / (2S)-2-aminopropan-1-ol


Mass: 75.110 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#51: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2
#52: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#53: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#54: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1TFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosomeCOMPLEX#1-#490MULTIPLE SOURCES
2General transcription factor IIHCOMPLEX#1-#101RECOMBINANT
3Mammalian RNA polymerase IICOMPLEX#11-#14, #28-#351NATURAL
4Nucleosome (protein)COMPLEX#46-#491RECOMBINANT
5Nucleosome (DNA)COMPLEX#37, #411RECOMBINANT
6General transcription factor IIBCOMPLEX#361RECOMBINANT
7Transcription initiation factor IIDCOMPLEX#15-#27, #381RECOMBINANT
8General transcription factor IIFCOMPLEX#39-#401RECOMBINANT
9General transcription factor IIACOMPLEX#42-#431RECOMBINANT
10General transcription factor IIECOMPLEX#44-#451RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.7 MDaNO
220.490 MDaNO
330.516 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Sus scrofa (pig)9823
34Xenopus laevis (African clawed frog)8355
45unidentified adenovirus10535
56Homo sapiens (human)9606
67Homo sapiens (human)9606
78Homo sapiens (human)9606
89Homo sapiens (human)9606
910Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
34Escherichia coli (E. coli)562
45synthetic construct (others)32630
56Escherichia coli (E. coli)562
67Trichoplusia ni (cabbage looper)7111
78Escherichia coli (E. coli)562
89Trichoplusia ni (cabbage looper)7111
910Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 88900
EM imaging opticsEnergyfilter name: GIF Quantum SE / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2SerialEM4image acquisition
4cryoSPARC4.7.1CTF correction
7UCSF ChimeraX1.9model fitting
9cryoSPARC4.7.1initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13ISOLDE1.9model refinement
14PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12714020
3D reconstructionResolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30253 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 814.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067129270
ELECTRON MICROSCOPYf_angle_d1.1676176747
ELECTRON MICROSCOPYf_chiral_restr0.063319746
ELECTRON MICROSCOPYf_plane_restr0.010921219
ELECTRON MICROSCOPYf_dihedral_angle_d16.247149969

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