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- PDB-5iyb: Human core-PIC in the open state -

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Entry
Database: PDB / ID: 5iyb
TitleHuman core-PIC in the open state
Components
  • (DNA-directed RNA polymerase II subunit ...) x 12
  • (General transcription factor IIF subunit ...) x 2
  • (Transcription initiation factor ...) x 4
  • General transcription factor IIE subunit 1
  • SCP-X
  • SCP-Y
  • TATA-box-binding protein
  • Transcription elongation factor A protein 1
KeywordsTRANSCRIPTION / TRANSFERASE/DNA / initiation / RNA polymerase II / human / TRANSFERASE-DNA complex
Function / homology
Function and homology information


LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / RPAP3/R2TP/prefoldin-like complex ...LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / RPAP3/R2TP/prefoldin-like complex / transcription factor TFIIE complex / phosphatase activator activity / Cytosolic sensors of pathogen-associated DNA / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / TFIIF-class transcription factor complex binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / RNA Polymerase I Transcription Termination / transcription preinitiation complex / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / cell division site / mRNA Capping / protein acetylation / PIWI-interacting RNA (piRNA) biogenesis / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / mRNA Splicing - Minor Pathway / RNA polymerase II complex binding / acetyltransferase activity / RNA Polymerase I Transcription Initiation / viral transcription / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / aryl hydrocarbon receptor binding / nuclear-transcribed mRNA catabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / core promoter sequence-specific DNA binding / Formation of RNA Pol II elongation complex / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / Inhibition of DNA recombination at telomere / TBP-class protein binding / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / SIRT1 negatively regulates rRNA expression / protein-DNA complex
Similarity search - Function
Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / RNA Polymerase II, Rpb4 subunit / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily ...Transcription factor IIA gamma subunit, alpha-helical domain / TATA box binding Protein, subunit D; domain 2 / Transcription factor IIA (TFIIA), beta-barrel domain / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / RNA Polymerase II, Rpb4 subunit / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / TATA-Binding Protein / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / RNA polymerase Rpb7-like, N-terminal domain / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / 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. / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / TFIIS/LEDGF domain superfamily / N-terminal domain of TfIIb - #10 / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / TBP domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / TATA-box-binding protein / Transcription elongation factor A protein 1 / DNA-directed RNA polymerase II subunit RPB1 / General transcription factor IIE subunit 1 ...DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB4 / General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / TATA-box-binding protein / Transcription elongation factor A protein 1 / DNA-directed RNA polymerase II subunit RPB1 / General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB2 / General transcription factor IIF subunit 1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHe, Y. / Yan, C. / Fang, J. / Inouye, C. / Tjian, R. / Ivanov, I. / Nogales, E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM63072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110387 United States
National Science Foundation (NSF, United States)MCB-1149521 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2016
Title: Near-atomic resolution visualization of human transcription promoter opening.
Authors: Yuan He / Chunli Yan / Jie Fang / Carla Inouye / Robert Tjian / Ivaylo Ivanov / Eva Nogales /
Abstract: In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the ...In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerase II subunit RPB5
F: DNA-directed RNA polymerase II subunit RPB6
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerase II subunit RPB8
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerase II subunit RPB10
K: DNA-directed RNA polymerase II subunit RPB11-a
L: DNA-directed RNA polymerase II subunit RPB12
M: Transcription initiation factor IIB
N: Transcription initiation factor IIA subunit 1
O: Transcription initiation factor IIA subunit 2
P: TATA-box-binding protein
Q: General transcription factor IIE subunit 1
R: Transcription initiation factor IIE subunit beta
S: General transcription factor IIF subunit 1
T: General transcription factor IIF subunit 2
U: Transcription elongation factor A protein 1
X: SCP-X
Y: SCP-Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)894,46536
Polymers893,69723
Non-polymers76813
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area123080 Å2
ΔGint-603 kcal/mol
Surface area261240 Å2

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Components

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DNA-directed RNA polymerase II subunit ... , 12 types, 12 molecules ABCDEFGHIJKL

#1: 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
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA ...DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA polymerase II subunit 2 / RNA polymerase II subunit B2


Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30876, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA- ...RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31


Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19387
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa ...RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15514
#5: Protein DNA-directed RNA polymerase II subunit RPB5 / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA DNA-directed RNA polymerases I / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA DNA-directed RNA polymerases I / II / and III subunit RPABC1 / polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / XAP4


Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19388
#6: Protein DNA-directed RNA polymerase II subunit RPB6 / DNA-directed RNA polymerases I / II / and III subunit RPABC2 / RNA polymerases I / II / and III ...DNA-directed RNA polymerases I / II / and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPC15


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa ...RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62487
#8: Protein DNA-directed RNA polymerase II subunit RPB8 / DNA-directed RNA polymerases I / II / and III subunit RPABC3 / RNA polymerases I / II / and III ...DNA-directed RNA polymerases I / II / and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / II / and III 17.1 kDa polypeptide / RPB17 / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52434
#9: 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) Homo sapiens (human) / References: UniProt: P36954
#10: Protein DNA-directed RNA polymerase II subunit RPB10 / DNA-directed RNA polymerases I / II / and III subunit RPABC5 / RNA polymerases I / II / and III ...DNA-directed RNA polymerases I / II / and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875
#11: Protein DNA-directed RNA polymerase II subunit RPB11-a / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52435
#12: Protein DNA-directed RNA polymerase II subunit RPB12 / DNA-directed RNA polymerases I / II / and III subunit RPABC4 / RNA polymerases I / II / and III ...DNA-directed RNA polymerases I / II / and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P53803

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

#13: 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
#14: Protein Transcription initiation factor IIA subunit 1 / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa ...General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42


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


Mass: 12469.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657
#18: 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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Protein , 3 types, 3 molecules PQU

#16: 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: Escherichia coli (E. coli) / References: UniProt: P20226
#17: 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
#21: Protein Transcription elongation factor A protein 1 / Transcription elongation factor S-II protein 1 / Transcription elongation factor TFIIS.o


Mass: 34022.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEA1, GTF2S, TFIIS / Production host: Escherichia coli (E. coli) / References: UniProt: P23193

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

#19: 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
#20: 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

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DNA chain , 2 types, 2 molecules XY

#22: DNA chain SCP-X


Mass: 23372.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#23: DNA chain SCP-Y


Mass: 22908.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 13 molecules

#24: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#25: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn

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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
1Human core-PIC in the open stateCOMPLEX#1-#230MULTIPLE SOURCES
2RNA polymerase IICOMPLEX#1-#121NATURAL
3General transcription factorsCOMPLEX#13-#211MULTIPLE SOURCES
4Super core promoterCOMPLEX#22-#231MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.90 MDaNO
220.52 MDaNO
330.33 MDaNO
440.06 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
13Escherichia coli (E. coli)562unknown
24Escherichia coli (E. coli)562unknown
Buffer solutionpH: 7.9
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).

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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 magnification: 27500 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30

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Processing

EM softwareName: RELION / Version: 1.4beta / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79849 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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