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- PDB-6o9l: Human holo-PIC in the closed state -

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Entry
Database: PDB / ID: 6o9l
TitleHuman holo-PIC in the closed state
Components
  • (DNA (65-MER)) x 2
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 8
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 4
  • (General transcription factor IIF subunit ...) x 2
  • (General transcription factor IIH subunit ...) x 5
  • (TFIIH basal transcription factor complex helicase ...) x 2
  • (Transcription initiation factor ...) x 4
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-H
  • Cyclin-dependent kinase 7
  • General transcription factor IIE subunit 1
  • TATA-box-binding protein
  • Transcription elongation factor A protein 1
KeywordsTRANSCRIPTION/DNA / Transcription initiation / Molecular dynamics / Gene regulation / Community network analysis / Global protein dynamics / RNA polymerase / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Formation of HIV-1 elongation complex containing HIV-1 Tat / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / Regulation of TP53 Activity through Phosphorylation / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / Cyclin E associated events during G1/S transition ...Formation of HIV-1 elongation complex containing HIV-1 Tat / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / Regulation of TP53 Activity through Phosphorylation / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / Cyclin E associated events during G1/S transition / Cyclin D associated events in G1 / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Cytosolic sensors of pathogen-associated DNA / HIV elongation arrest and recovery / MicroRNA (miRNA) biogenesis / Cytosolic iron-sulfur cluster assembly / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Tat-mediated elongation of the HIV-1 transcript / Tat-mediated HIV elongation arrest and recovery / Abortive elongation of HIV-1 transcript in the absence of Tat / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / PIWI-interacting RNA (piRNA) biogenesis / Pausing and recovery of Tat-mediated HIV elongation / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Transcription of the HIV genome / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Polymerase II Pre-transcription Events / Formation of the HIV-1 Early Elongation Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / Viral Messenger RNA Synthesis / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Termination / mRNA Capping / RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Signaling by FGFR2 IIIa TM / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Pausing and recovery of HIV elongation / rt:r-hsa-73777: / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / mRNA Splicing - Minor Pathway / mRNA Splicing - Major Pathway / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase III Chain Elongation / cyclin-dependent protein kinase activating kinase holoenzyme complex / transcription factor TFIIK complex / positive regulation of exoribonuclease activity / ventricular system development / negative regulation of DNA helicase activity / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA polymerase II core complex assembly / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / 5'-3' DNA helicase activity / regulation of mitotic recombination / erythrocyte maturation / transcription factor TFIIE complex / hair follicle maturation / nucleotide-excision repair factor 3 complex / phosphatase activator activity / adult heart development / hair cell differentiation / transcription factor TFIIH core complex / transcriptional open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIH holo complex / embryonic cleavage / TFIIH-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II complex recruiting activity / 3'-5' DNA helicase activity / ec:2.7.11.23: / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / transcription factor TFIIIB complex / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / regulation of transcription by RNA polymerase I
RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / Ssl1-like / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 ...RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / Ssl1-like / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 6 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 / Helicase/UvrB, N-terminal / Cyclin, N-terminal / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / RNA polymerase Rpb2, domain 5 / Serine/threonine-protein kinase, active site / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / PH-like domain superfamily / Zinc finger, TFIIB-type / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / ATP-dependent helicase Rad3/Chl1-like / Nucleic acid-binding, OB-fold / TBP domain superfamily / RNA polymerase subunit, RPB6/omega / TFIIH subunit Ssl1/p44 / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Transcription initiation factor IIF, alpha subunit / DNA-directed RNA polymerase, insert domain / Transcription Factor IIF, Rap30/Rap74, interaction / Protein kinase-like domain superfamily / HRDC-like superfamily / Helical and beta-bridge domain / DEAD2 / TFIIH subunit TTDA/Tfb5 / Transcription factor IIA, beta-barrel / Transcription factor IIA, helical / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription elongation factor, TFIIS / RNA polymerase, subunit omega/K/RPB6 / Cyclin-like / Type III restriction enzyme, res subunit / Helicase XPB/Ssl2 / TATA-box binding protein / Transcription factor TFIIB / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / Protein kinase domain / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription factor TFIIH complex subunit Tfb5 / Zinc finger, TFIIS-type / DNA-directed RNA polymerase, M/15kDa subunit / BSD domain / Ubiquitin interacting motif / RNA polymerase Rpb7-like , N-terminal / RNA polymerase subunit RPB4/RPC9 / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / Transcription factor IIA, alpha/beta subunit / TFIIH subunit Tfb4/GTF2H3 / Transcription factor TFIIH subunit p52/Tfb2 / TFIIH C1-like domain / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription elongation factor S-II, central domain / Helicase, C-terminal / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Transcription initiation factor IIF, beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIE beta subunit, DNA-binding domain / S1 domain / Transcription initiation factor IIE subunit alpha, N-terminal / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / von Willebrand factor, type A / RAD3/XPD family / Zinc finger, RING-type / Transcription factor TFIIB, cyclin-like domain / TFIIH p62 subunit, N-terminal / DEAD_2 / TFIIF, beta subunit, N-terminal
General transcription factor IIH subunit 5 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 2 / Transcription initiation factor IIB / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 ...General transcription factor IIH subunit 5 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 2 / Transcription initiation factor IIB / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / CDK-activating kinase assembly factor MAT1 / Cyclin-H / DNA-directed RNA polymerase II subunit RPB9 / Cyclin-dependent kinase 7 / General transcription factor IIF subunit 1 / General transcription factor IIH subunit 1 / DNA-directed RNA polymerase II subunit RPB2 / Transcription initiation factor IIE subunit beta / General transcription factor IIE subunit 1 / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor A protein 1 / TATA-box-binding protein / General transcription and DNA repair factor IIH helicase subunit XPB / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription factor IIF subunit 2 / DNA-directed RNA polymerase II subunit RPB4 / General transcription factor IIH subunit 4
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsYan, C.L. / Dodd, T. / He, Y. / Tainer, J.A. / Tsutakawa, S.E. / Ivanov, I.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM110387United States
CitationJournal: Nature / Year: 2016
Title: Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.
Authors: Robert K Louder / Yuan He / José Ramón López-Blanco / Jie Fang / Pablo Chacón / Eva Nogales /
Abstract: The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the ...The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 14, 2019 / Release: May 29, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 29, 2019Structure modelrepositoryInitial release
1.1Jun 5, 2019Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Jun 19, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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 polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
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
0: TFIIH basal transcription factor complex helicase XPD subunit
1: General transcription factor IIH subunit 1
2: General transcription factor IIH subunit 4, p52
3: CDK-activating kinase assembly factor MAT1
4: General transcription factor IIH subunit 3
5: General transcription factor IIH subunit 5
6: General transcription factor IIH subunit 2
7: TFIIH basal transcription factor complex helicase XPB subunit
8: Cyclin-dependent kinase 7
9: Cyclin-H
X: DNA (65-MER)
Y: DNA (65-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,379,41653
Polymers1,377,90433
Non-polymers1,51220
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area184510 Å2
ΔGint-1132 kcal/mol
Surface area497050 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ABCDEGIK

#1: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase / 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, EC: 2.7.7.6, EC: 2.7.7.48
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB2 / Polymerase / 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, EC: 2.7.7.6
#3: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / 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/peptide DNA-directed RNA polymerase II subunit RPB4 / Polymerase / 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/peptide DNA-directed RNA polymerase II subunit RPB5 / Polymerase / 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
#7: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / 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
#9: Protein/peptide 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 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
#11: Protein/peptide DNA-directed RNA polymerase II subunit RPB11-a / Polymerase / 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

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DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules FHJL

#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / 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 / RPB6 homolog / RPC15


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218
#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


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


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / 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/peptide 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, EC: 2.3.1.48
#14: Protein/peptide Transcription initiation factor IIA subunit 1 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52655
#15: Protein/peptide Transcription initiation factor IIA subunit 2 / 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/peptide 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/peptide , 6 types, 6 molecules PQU389

#16: Protein/peptide TATA-box-binding protein / 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/peptide General transcription factor IIE subunit 1 / 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/peptide 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P23193
#25: Protein/peptide CDK-activating kinase assembly factor MAT1 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51948
#30: Protein/peptide Cyclin-dependent 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50613, EC: 2.7.11.22, EC: 2.7.11.23
#31: Protein/peptide Cyclin-H / MO15-associated protein / p34 / p37


Mass: 37695.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51946

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

#19: Protein/peptide General transcription factor IIF subunit 1 / 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/peptide General transcription factor IIF subunit 2 / 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, EC: 3.6.4.12

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TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules 07

#22: Protein/peptide TFIIH basal transcription factor complex helicase XPD subunit / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 87021.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Escherichia coli (E. coli) / References: UniProt: P18074, EC: 3.6.4.12
#29: Protein/peptide TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 89404.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19447, EC: 3.6.4.12

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General transcription factor IIH subunit ... , 5 types, 5 molecules 12456

#23: Protein/peptide General transcription factor IIH subunit 1 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32780
#24: Protein/peptide General transcription factor IIH subunit 4, p52 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92759
#26: Protein/peptide General transcription factor IIH subunit 3 / p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13889
#27: Protein/peptide General transcription factor IIH subunit 5 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6ZYL4
#28: Protein/peptide General transcription factor IIH subunit 2 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13888

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DNA chain , 2 types, 2 molecules XY

#32: DNA chain DNA (65-MER)


Mass: 20214.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain DNA (65-MER)


Mass: 19867.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 20 molecules

#34: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Iron–sulfur cluster

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: holo-PIC in the closed state / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33
Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
12NAMD2.12model fittingMolecular dynamics flexible fitting
13UCSF Chimera1.12model fittingRigid body fit
20Coot0.8.9.1model refinementmodel building and refinement
21PHENIX1.14model refinementreal-space refinement
3D reconstructionResolution: 7.2 Å / Num. of particles: 24290
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Initial model assembled from high-resolution structures and homology models, subsequently rebuilt in COOT, refined into the Cryo-EM map using Phenix and fully validated.

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