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- PDB-7edx: p53-bound TFIID-based core PIC on HDM2 promoter -

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Basic information

Entry
Database: PDB / ID: 7edx
Titlep53-bound TFIID-based core PIC on HDM2 promoter
Components
  • (DNA (84-mer)) x 2
  • (DNA-directed RNA ...) x 8
  • (General transcription factor IIF subunit ...) x 2
  • (Transcription initiation factor IIA subunit ...) x 2
  • (Transcription initiation factor TFIID subunit ...) x 13
  • RNA_pol_L_2 domain-containing protein
  • RPB10
  • RPB12
  • RPB1POLR2A
  • TATA-box-binding protein
  • Transcription initiation factor IIB
KeywordsTRANSCRIPTION / TFIID / preinitiation complex / core promoter / transcription initiation
Function / homology
Function and homology information


negative regulation of MHC class I biosynthetic process / spermine transport / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / pre-snoRNP complex / SAGA complex => GO:0000124 / RNA polymerase II core complex assembly / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs ...negative regulation of MHC class I biosynthetic process / spermine transport / TFIIH-class transcription factor complex binding / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / pre-snoRNP complex / SAGA complex => GO:0000124 / RNA polymerase II core complex assembly / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / Formation of the Early Elongation Complex / mRNA Splicing - Minor Pathway / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major 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 Pol II CTD phosphorylation and interaction with CE / RNA Polymerase II Transcription Initiation And Promoter Clearance / Formation of RNA Pol II elongation complex / transcription factor TFTC complex / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of MHC class II biosynthetic process / SAGA complex => GO:0000124 / phosphatase activator activity / TFIIF-class transcription factor complex binding / regulation of cell cycle G1/S phase transition / SLIK (SAGA-like) complex / positive regulation of core promoter binding / regulation of DNA binding / transcription factor TFIIF complex / RNA polymerase I general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / SAGA complex / transcription regulator inhibitor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / positive regulation of response to cytokine stimulus / RNA Polymerase III Abortive And Retractive Initiation / inner cell mass cell proliferation / RNA polymerase II-specific DNA-binding transcription factor binding / maintenance of protein location in nucleus / RNA polymerase III general transcription initiation factor activity / histone deubiquitination / hepatocyte differentiation / transcription factor TFIIA complex / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of androgen receptor activity / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / box C/D snoRNP assembly / transcription factor catabolic process / C2H2 zinc finger domain binding / positive regulation by host of viral transcription / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / FGFR2 alternative splicing / male pronucleus / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / female pronucleus / Viral Messenger RNA Synthesis / mRNA Capping / RNA polymerase binding / positive regulation of viral transcription / thyroid hormone receptor binding / transcription initiation from RNA polymerase I promoter / vitamin D receptor binding / RNA polymerase II preinitiation complex assembly / Processing of Capped Intron-Containing Pre-mRNA / midbrain development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation / regulation of fat cell differentiation / termination of RNA polymerase I transcription / RNA polymerase complex / Signaling by FGFR2 IIIa TM / Tat-mediated HIV elongation arrest and recovery / Pausing and recovery of Tat-mediated HIV elongation / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / Pausing and recovery of HIV elongation / HIV elongation arrest and recovery
Similarity search - Function
TAFII28-like protein domain / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / 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 ...TAFII28-like protein domain / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein, conserved region / TAFII55 protein conserved region / Transcription initiation factor TFIID subunit 7 / 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 family / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor IID, subunit 13 / Transcription initiation factor TFIID component TAF4, C-terminal / NHR1 homology to TAF / TAF homology / Bromodomain transcription factors and PHD domain containing proteins / TAFH/NHR1 domain superfamily / Bromodomain associated / TAFH/NHR1 domain profile. / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 12 / TAFH/NHR1 / Transcription initiation factor TFIID subunit 5 / 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 / TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / TATA box-binding protein binding / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / Zinc knuckle / Zinc knuckle / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 1, domain of unknown function / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / LIS1 homology (LisH) motif profile. / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit / LIS1 homology motif / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / TBP domain superfamily / Aminopeptidase N-like , N-terminal / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / Cyclin-like / RNA polymerase Rpb2, domain 5 / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 10 / 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 7 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 ...Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 10 / 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 7 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 2 / General transcription factor IIF subunit 1 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 6 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor TFIID subunit 1 / TATA-box-binding protein / General transcription factor IIF subunit 2 / Transcription initiation factor TFIID subunit 4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerase subunit beta / Uncharacterized protein / DNA-directed RNA polymerase II subunit RPB4 / : / DNA (> 10) / DNA / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsChen, X. / Qi, Y. / Hou, H. / Wang, X. / Wu, Z. / Li, J. / Xu, Y.
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 17, 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

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Structure visualization

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Assembly

Deposited unit
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
X: DNA (84-mer)
Y: DNA (84-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: 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
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
u: DNA-directed RNA polymerase II subunit RPB7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,026,51949
Polymers2,025,90639
Non-polymers61310
Water0
1


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

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Components

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Transcription initiation factor TFIID subunit ... , 13 types, 19 molecules ABDdEeFfGHIiJjLlckm

#1: 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
#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#19: 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
#20: 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
#21: 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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Transcription initiation factor IIA subunit ... , 2 types, 2 molecules OQ

#11: 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
#13: 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

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Protein , 6 types, 6 molecules PRoxyz

#12: 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
#14: 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
#22: Protein RPB1 / POLR2A


Mass: 217420.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
#30: Protein RPB10


Mass: 7655.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
#31: Protein RNA_pol_L_2 domain-containing protein


Mass: 13310.284 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2J / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1UK25
#32: Protein RPB12


Mass: 7018.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2K / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1TRS6

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

#15: 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
#16: 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

#17: DNA chain DNA (84-mer)


Mass: 26001.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 904033
#18: DNA chain DNA (84-mer)


Mass: 25815.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 904033

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DNA-directed RNA ... , 8 types, 8 molecules pqrstvwu

#23: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 134041.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
References: UniProt: A0A4X1TVZ5, DNA-directed RNA polymerase
#24: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit C


Mass: 31439.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2C / Production host: Sus scrofa (pig) / References: UniProt: I3LCH3
#25: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / DNA-directed RNA polymerase II subunit RPB4 isoform X1


Mass: 16331.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig) / References: UniProt: A0A481BYI6
#26: Protein DNA-directed RNA polymerase II subunit E / Polymerase / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2E / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VTX4
#27: 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2F / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VEK9
#28: 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2H / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1ULF2
#29: 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 genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2I / Production host: Sus scrofa (pig) / References: UniProt: P60899
#33: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase


Mass: 19314.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: POLR2G / Production host: Sus scrofa (pig) / References: UniProt: A0A4X1VKG7

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Non-polymers , 2 types, 10 molecules

#34: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 9 / 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

Component
IDNameTypeEntity IDParent-IDSource
1p53-bound TFIID-based core PIC on HDM2 promoterCOMPLEX#1-#330MULTIPLE SOURCES
2TFIIDTranscription factor II DCOMPLEX#1-#10, #12, #19-#211RECOMBINANT
3RNA POLYMERASE IICOMPLEX#22-#331RECOMBINANT
4TFIIATranscription factor II ACOMPLEX#11, #131RECOMBINANT
5TFIIBTranscription factor II BCOMPLEX#141RECOMBINANT
6TFIIFTranscription factor II FCOMPLEX#15-#161RECOMBINANT
7DNA(SCP promoters)COMPLEX#17-#181SYNTHETIC
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
33Sus scrofa (pig)9823HEK293T
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 FIELDBright-field microscopy
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99580 / Symmetry type: POINT

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