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- PDB-7ml2: RNA polymerase II pre-initiation complex (PIC3) -

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Basic information

Entry
Database: PDB / ID: 7ml2
TitleRNA polymerase II pre-initiation complex (PIC3)
Components
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (DNA-directed RNA polymerases II subunit ...) x 2
  • (General transcription and DNA repair factor ...) x 4
  • (Transcription initiation factor IIA ...) x 2
  • (Transcription initiation factor IIE subunit ...) x 2
  • (Transcription initiation factor IIF subunit ...) x 2
  • BJ4_G0004860.mRNA.1.CDS.1
  • BJ4_G0050160.mRNA.1.CDS.1
  • DNA-directed RNA polymerases I,II,and III subunit RPABC2
  • RNA polymerase II transcription factor B subunit 2
  • Tfb1
  • Tfb4
  • Transcription initiation factor IIB
  • non-template strand DNA
  • template strand DNA
KeywordsTRANSCRIPTION / PIC / TFIIH / ITC / RNA polymerase II
Function / homology
Function and homology information


: / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / : / TFIIH-class transcription factor complex binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex ...: / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / : / TFIIH-class transcription factor complex binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIA complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription preinitiation complex / 3'-5' DNA helicase activity / Processing of Capped Intron-Containing Pre-mRNA / DNA 3'-5' helicase / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / ATPase activator activity / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / protein phosphatase activator activity / Dual incision in TC-NER / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / DNA helicase activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-directed RNA polymerase activity / isomerase activity / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / DNA-directed RNA polymerase / single-stranded DNA binding / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / nucleic acid binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / single-stranded RNA binding / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / protein-containing complex / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / Bacterial type XPD DNA helicase, FeS cluster domain / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain ...: / Bacterial type XPD DNA helicase, FeS cluster domain / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Gyrase A; domain 2 - #140 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / 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 / 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. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / TFIIB zinc-binding / 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 Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / Enzyme I; Chain A, domain 2 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / TBP domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIE subunit beta / RPB4 isoform 1 / TFA1 isoform 1 / RPC10 isoform 1 / TFG2 isoform 1 / RPB3 isoform 1 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIE subunit beta / RPB4 isoform 1 / TFA1 isoform 1 / RPC10 isoform 1 / TFG2 isoform 1 / RPB3 isoform 1 / General transcription and DNA repair factor IIH helicase subunit XPD / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit / TOA1 isoform 1 / RNA polymerase II transcription factor B subunit 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase subunit beta / RPB11 isoform 1 / RPB10 isoform 1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase II transcription factor B subunit 3 / DNA-directed RNA polymerase subunit / TATA-binding protein / Transcription initiation factor IIB / Transcription initiation factor IIF subunit alpha / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYang, C. / Fujiwara, R. / Kim, H.J. / Gorbea Colon, J.J. / Steimle, S. / Garcia, B.A. / Murakami, K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA196539 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG031862 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023592 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami /
Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
History
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / em_entity_assembly_molwt / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _em_entity_assembly_molwt.entity_assembly_id / _em_entity_assembly_molwt.id / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I,II,and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases II subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases II subunit RPABC4
M: Transcription initiation factor IIB
Q: Transcription initiation factor IIF subunit alpha
R: Transcription initiation factor IIF subunit beta
U: Transcription initiation factor IIA large subunit
V: Transcription initiation factor IIA subunit 2
W: Transcription initiation factor IIE subunit alpha
X: Transcription initiation factor IIE subunit beta
T: template strand DNA
N: non-template strand DNA
O: BJ4_G0004860.mRNA.1.CDS.1
1: Tfb1
4: Tfb4
0: General transcription and DNA repair factor IIH helicase subunit XPD
6: General transcription and DNA repair factor IIH
2: RNA polymerase II transcription factor B subunit 2
5: General transcription and DNA repair factor IIH subunit TFB5
7: General transcription and DNA repair factor IIH helicase subunit XPB
3: BJ4_G0050160.mRNA.1.CDS.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,320,45549
Polymers1,318,96830
Non-polymers1,48819
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assembly was confirmed by glycerol gradient sedimentation followed by SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA-directed RNA polymerase ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase subunit


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q1P2, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q4H2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z3
#4: Protein DNA-directed RNA polymerase II subunit RPB4


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTI6
#7: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q270
#9: Protein DNA-directed RNA polymerase II subunit RPB9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9EWC2
#11: Protein DNA-directed RNA polymerase II subunit RPB11


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7A1

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DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q456
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8C2

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Protein , 7 types, 7 molecules FMO1423

#6: Protein DNA-directed RNA polymerases I,II,and III subunit RPABC2


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZRI7
#13: Protein Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


Mass: 38257.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29055
#22: Protein BJ4_G0004860.mRNA.1.CDS.1 / BJ4_G0016160.mRNA.1.CDS.1 / EM14S01-3B_G0002200.mRNA.1.CDS.1 / HLJ1_G0002280.mRNA.1.CDS.1 / JXXY16_ ...BJ4_G0016160.mRNA.1.CDS.1 / EM14S01-3B_G0002200.mRNA.1.CDS.1 / HLJ1_G0002280.mRNA.1.CDS.1 / JXXY16_1_G0002270.mRNA.1.CDS.1 / SX2_G0002280.mRNA.1.CDS.1 / TATA-binding protein / TATA-box-binding protein / XXYS1_4_G0005080.mRNA.1.CDS.1 / Y55_G0002290.mRNA.1.CDS.1


Mass: 27042.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G4XSG8
#23: Protein Tfb1


Mass: 58593.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein Tfb4


Mass: 37430.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#27: Protein RNA polymerase II transcription factor B subunit 2


Mass: 58602.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2X3
#30: Protein BJ4_G0050160.mRNA.1.CDS.1 / SX2_G0047880.mRNA.1.CDS.1 / Y55_G0047830.mRNA.1.CDS.1


Mass: 38188.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A7I9BTI9

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DNA-directed RNA polymerases II subunit ... , 2 types, 2 molecules JL

#10: Protein DNA-directed RNA polymerases II subunit RPABC5


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7Q6
#12: Protein DNA-directed RNA polymerases II subunit RPABC4


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PY05

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Transcription initiation factor IIF subunit ... , 2 types, 2 molecules QR

#14: Protein Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


Mass: 82320.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41895
#15: Protein Transcription initiation factor IIF subunit beta


Mass: 46684.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZ00

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Transcription initiation factor IIA ... , 2 types, 2 molecules UV

#16: Protein Transcription initiation factor IIA large subunit / Y55_G0039490.mRNA.1.CDS.1


Mass: 32230.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2T8
#17: Protein Transcription initiation factor IIA subunit 2


Mass: 13473.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PRZ0

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Transcription initiation factor IIE subunit ... , 2 types, 2 molecules WX

#18: Protein Transcription initiation factor IIE subunit alpha


Mass: 54804.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTU5
#19: Protein Transcription initiation factor IIE subunit beta


Mass: 37050.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PS93

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DNA chain , 2 types, 2 molecules TN

#20: DNA chain template strand DNA


Mass: 17166.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#21: DNA chain non-template strand DNA


Mass: 17336.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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General transcription and DNA repair factor ... , 4 types, 4 molecules 0657

#25: Protein General transcription and DNA repair factor IIH helicase subunit XPD / Rad3


Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1C1, DNA helicase
#26: Protein General transcription and DNA repair factor IIH


Mass: 52024.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein General transcription and DNA repair factor IIH subunit TFB5 / TFIIH subunit TFB5 / RNA polymerase II transcription factor B subunit 5


Mass: 8243.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7C1
#29: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / DNA repair helicase RAD25 / RNA polymerase II transcription factor B subunit ...TFIIH subunit XPB / DNA repair helicase RAD25 / RNA polymerase II transcription factor B subunit SSL2 / TFB subunit SSL2 / Suppressor of stem-loop mutation 2


Mass: 95461.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q00578, DNA helicase

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Non-polymers , 3 types, 19 molecules

#31: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#32: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1RNA polymerase II pre-initiation complex (PIC3)COMPLEXcomposite map assembled from 3 independently refined domains#1-#300NATURAL
2Pol II + TFIIBCOMPLEX#1-#131NATURAL
3DNA+TBP+TFIIA+TFIIE+TFIIFCOMPLEX#14-#221NATURAL
4TFIIHCOMPLEX#23-#301NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
33NO
44
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
43Saccharomyces cerevisiae (brewer's yeast)4932
54Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
12RELION3.1classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69513
Details: Final map is a composite of 3 separately refined domains.
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5OQJ

5oqj


Accession code: 5OQJ / Source name: PDB / Type: experimental model

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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