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- PDB-7egb: TFIID-based holo PIC on SCP promoter -

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Basic information

Entry
Database: PDB / ID: 7egb
TitleTFIID-based holo PIC on SCP promoter
Components
  • (DNA (69-MER)) x 2
  • (DNA-directed RNA ...) x 9
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription factor IIF subunit ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • (Transcription initiation factor ...) x 17
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
  • General transcription factor IIE subunit 1
  • RNA_pol_L_2 domain-containing protein
  • RPB10
  • RPB12
  • TATA-box-binding protein
KeywordsTRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation
Function / homology
Function and homology information


negative regulation of MHC class I biosynthetic process / microfibril binding / spermine transport / MMXD complex / core TFIIH complex portion of holo TFIIH complex / SAGA complex assembly / lateral mesodermal cell differentiation / DNA-templated transcription open complex formation / allantois development / pre-snoRNP complex ...negative regulation of MHC class I biosynthetic process / microfibril binding / spermine transport / MMXD complex / core TFIIH complex portion of holo TFIIH complex / 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 / Cytosolic iron-sulfur cluster assembly / TFIIH-class transcription factor complex binding / central nervous system myelin formation / negative regulation of protein autoubiquitination / positive regulation of core promoter binding / negative regulation of MHC class II biosynthetic process / transcription factor TFTC complex / RNA polymerase II core complex assembly / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / transcription factor TFIIE complex / nucleotide-excision repair factor 3 complex / RNA polymerase transcription factor SL1 complex / nucleotide-excision repair, preincision complex assembly / meiotic sister chromatid cohesion / phosphatase activator activity / ventricular system development / SLIK (SAGA-like) complex / histone H4K16ac reader activity / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / transcription factor TFIIK complex / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / UV protection / hepatocyte differentiation / transcription factor TFIIF complex / embryonic cleavage / positive regulation of response to cytokine stimulus / DNA 5'-3' helicase / 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 / 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 / transcription factor TFIIA complex / adult heart development / maintenance of protein location in nucleus / C2H2 zinc finger domain binding / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / regulation of cyclin-dependent protein serine/threonine kinase activity / G protein-coupled receptor internalization / histone H3K4me3 reader activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / male pronucleus / host-mediated activation of viral transcription / cyclin-dependent protein serine/threonine kinase activator activity / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear vitamin D receptor binding / RNA polymerase binding / nuclear thyroid hormone receptor binding / regulation of fat cell differentiation / [RNA-polymerase]-subunit kinase / limb development / box C/D snoRNP assembly / SAGA complex / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination
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 / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 ...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 / 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 / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / : / Transcription initiation factor IID, 31kD subunit / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TFIID subunit TAF5, NTD2 domain superfamily / WD40 associated region in TFIID subunit, NTD2 domain / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 12 domain / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat 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) / 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 / CyclinH/Ccl1 / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / Cyclin-dependent kinase 7 / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Cdk-activating kinase assembly factor MAT1/Tfb3
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase subunit ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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 II subunit RPB3 / Transcription initiation factor TFIID subunit 4 / 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 / DNA-directed RNA polymerase II subunit RPB1 / 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 / 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 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 2 / General transcription factor IIH subunit 5 / Transcription initiation factor TFIID subunit 8 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen, X. / Wu, Z. / Hou, H. / Qi, Y. / Wang, X. / Li, J. / Xu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2021
Title: Structural insights into preinitiation complex assembly on core promoters.
Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu /
Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
History
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / database_2 / em_imaging / em_software / entity / entity_src_gen / entity_src_nat / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _entity_src_nat.common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
0: CDK-activating kinase assembly factor MAT1
1: General transcription factor IIH subunit 1
2: General transcription factor IIH subunit 2
3: General transcription factor IIH subunit 3
4: General transcription factor IIH subunit 4
5: General transcription factor IIH subunit 5
6: General transcription and DNA repair factor IIH helicase subunit XPB
7: General transcription and DNA repair factor IIH helicase subunit XPD
8: Cyclin-dependent kinase 7
9: Cyclin-H
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 2
D: Transcription initiation factor TFIID subunit 4
E: Transcription initiation factor TFIID subunit 5
F: Transcription initiation factor TFIID subunit 6
G: Transcription initiation factor TFIID subunit 7
H: Transcription initiation factor TFIID subunit 8
I: Transcription initiation factor TFIID subunit 9
J: Transcription initiation factor TFIID subunit 10
L: Transcription initiation factor TFIID subunit 12
O: Transcription initiation factor IIA subunit 2
P: TATA-box-binding protein
Q: Transcription initiation factor IIA subunit 1
R: Transcription initiation factor IIB
S: General transcription factor IIF subunit 1
T: General transcription factor IIF subunit 2
U: General transcription factor IIE subunit 1
V: Transcription initiation factor IIE subunit beta
X: DNA (69-MER)
Y: DNA (69-MER)
c: Transcription initiation factor TFIID subunit 3
d: Transcription initiation factor TFIID subunit 4
e: Transcription initiation factor TFIID subunit 5
f: Transcription initiation factor TFIID subunit 6
i: Transcription initiation factor TFIID subunit 9
j: Transcription initiation factor TFIID subunit 10
k: Transcription initiation factor TFIID subunit 11
l: Transcription initiation factor TFIID subunit 12
m: Transcription initiation factor TFIID subunit 13
o: DNA-directed RNA polymerase II subunit RPB1
p: DNA-directed RNA polymerase subunit beta
q: DNA-directed RNA polymerase II subunit RPB3
r: DNA-directed RNA polymerase II subunit RPB4
s: DNA-directed RNA polymerase II subunit E
t: DNA-directed RNA polymerase II subunit F
u: DNA-directed RNA polymerase II subunit RPB7
v: DNA-directed RNA polymerases I, II, and III subunit RPABC3
w: DNA-directed RNA polymerase II subunit RPB9
x: RPB10
y: RNA_pol_L_2 domain-containing protein
z: RPB12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,598,88870
Polymers2,597,40051
Non-polymers1,48819
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 8 molecules 089PUxyz

#1: 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: Homo sapiens (human) / 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: Homo sapiens (human)
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: Homo sapiens (human) / References: UniProt: P51946
#22: 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: Homo sapiens (human) / References: UniProt: P20226
#27: 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: Homo sapiens (human) / References: UniProt: P29083
#43: Protein RPB10


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#44: 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
#45: Protein RPB12


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TRS6

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General transcription factor IIH subunit ... , 5 types, 5 molecules 12345

#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: Homo sapiens (human) / References: UniProt: P32780
#3: 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: Homo sapiens (human) / References: UniProt: Q13888
#4: 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: Homo sapiens (human) / References: UniProt: Q13889
#5: 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: Homo sapiens (human) / References: UniProt: Q92759
#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: Homo sapiens (human) / References: UniProt: Q6ZYL4

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General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 67

#7: 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 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: Homo sapiens (human) / References: UniProt: P19447, DNA helicase
#8: Protein General transcription and DNA repair factor IIH helicase subunit XPD / TFIIH subunit XPD / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision ...TFIIH subunit XPD / 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 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: Homo sapiens (human) / References: UniProt: P18074, DNA helicase

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Transcription initiation factor ... , 17 types, 23 molecules ABDdEeFfGHIiJjLlOQRVckm

#11: 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: 212956.172 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: Homo sapiens (human)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#12: 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: Homo sapiens (human) / References: UniProt: Q6P1X5
#13: 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: Homo sapiens (human) / References: UniProt: O00268
#14: 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, TAF2D / Production host: Homo sapiens (human) / References: UniProt: Q15542
#15: 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: Homo sapiens (human) / References: UniProt: P49848
#16: Protein Transcription initiation factor TFIID subunit 7 / RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa ...RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa subunit / TAF(II)55 / TAFII-55 / TAFII55


Mass: 40325.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, TAF2F, TAFII55 / Production host: Homo sapiens (human) / References: UniProt: Q15545
#17: 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: Homo sapiens (human) / References: UniProt: Q7Z7C8
#18: Protein Transcription initiation factor TFIID subunit 9 / RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor ...RNA polymerase II TBP-associated factor subunit G / STAF31/32 / Transcription initiation factor TFIID 31 kDa subunit / TAFII-31 / TAFII31 / Transcription initiation factor TFIID 32 kDa subunit / TAFII-32 / TAFII32


Mass: 29006.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF9, TAF2G, TAFII31 / Production host: Homo sapiens (human) / References: UniProt: Q16594
#19: 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: Homo sapiens (human) / References: UniProt: Q12962
#20: 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: Homo sapiens (human) / References: UniProt: Q16514
#21: 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: Homo sapiens (human) / References: UniProt: P52657
#23: 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: Homo sapiens (human) / References: UniProt: P52655
#24: 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: Homo sapiens (human) / References: UniProt: Q00403, histone acetyltransferase
#28: 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: Homo sapiens (human) / References: UniProt: P29084
#31: Protein Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription ...140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAF(II)140 / TAF140 / TAFII-140 / TAFII140


Mass: 103769.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF3 / Production host: Homo sapiens (human) / References: UniProt: Q5VWG9
#32: 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: Homo sapiens (human) / References: UniProt: Q15544
#33: 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, TAF2K, TAFII18 / Production host: Homo sapiens (human) / References: UniProt: Q15543

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General transcription factor IIF subunit ... , 2 types, 2 molecules ST

#25: 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: Homo sapiens (human) / References: UniProt: P35269
#26: 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: Homo sapiens (human) / References: UniProt: P13984, DNA helicase

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DNA chain , 2 types, 2 molecules XY

#29: DNA chain DNA (69-MER)


Mass: 29188.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#30: DNA chain DNA (69-MER)


Mass: 21094.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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DNA-directed RNA ... , 9 types, 9 molecules opqrstuvw

#34: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase
#35: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A4X1TVZ5, DNA-directed RNA polymerase
#36: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit C


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#37: Protein DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB4 isoform X1


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A481BYI6
#38: Protein 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
#39: Protein DNA-directed RNA polymerase II subunit F / 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: A0A4X1VEK9
#40: 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
#41: 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: A0A4X1ULF2
#42: 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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Non-polymers , 3 types, 19 molecules

#46: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#47: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#48: Chemical ChemComp-MG / MAGNESIUM ION


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

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Details

Has ligand of interestN
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-based holo PIC on SCP promoterCOMPLEX#1-#440MULTIPLE SOURCES
2TFIIDCOMPLEX#11-#20, #22, #31-#331RECOMBINANT
3RNA POLYMERASE IICOMPLEX#34-#441NATURAL
4TFIIACOMPLEX#21, #231RECOMBINANT
5TFIIBCOMPLEX#241RECOMBINANT
6TFIIFCOMPLEX#25-#261RECOMBINANT
7DNA(SCP promoters)COMPLEX#301SYNTHETIC
8TFIIHCOMPLEX#1-#91RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Sus scrofa (pig)9823
44Homo sapiens (human)9606
55Homo sapiens (human)9606
66Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606HEK239T
44Homo sapiens (human)9606HEK293T
55Homo sapiens (human)9606HEK293T
66Homo sapiens (human)9606HEK293T
Buffer solutionpH: 7.9
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92806 / Symmetry type: POINT

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