+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23908 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | RNA polymerase II initially transcribing complex (ITC) | ||||||||||||||||||
Map data | ITC | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding / 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 / transcription open complex formation at RNA polymerase II promoter / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / transcription preinitiation complex / DNA duplex unwinding / DNA binding, bending / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / 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 Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Estrogen-dependent gene expression / ATPase activator activity / acetyltransferase activity / transcription factor TFIID complex / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / DNA helicase activity / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / disordered domain specific binding / single-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription factor binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) / Baker's yeast (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Yang C / Fujiwara R / Kim HJ / Gorbea Colon JJ / Steimle S / Garcia BA / Murakami K | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23908.map.gz | 93 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23908-v30.xml emd-23908.xml | 54.3 KB 54.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23908_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_23908.png | 49.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23908 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23908 | HTTPS FTP |
-Validation report
Summary document | emd_23908_validation.pdf.gz | 352.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23908_full_validation.pdf.gz | 351.7 KB | Display | |
Data in XML | emd_23908_validation.xml.gz | 9 KB | Display | |
Data in CIF | emd_23908_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23908 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23908 | HTTPS FTP |
-Related structure data
Related structure data | 7ml4MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml2C 7ml3C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10865 (Title: Structural visualization of de novo initiation of RNA polymerase II transcription Data size: 14.3 TB Data #1: raw micrographs for PIC + ITC maps [micrographs - multiframe] Data #2: raw micrographs for EC+EC map [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23908.map.gz / Format: CCP4 / Size: 364.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ITC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : RNA polymerase II initially transcribing complex (ITC)
+Supramolecule #1: RNA polymerase II initially transcribing complex (ITC)
+Supramolecule #2: Pol II + TFIIB + RNA
+Supramolecule #3: DNA+TBP+TFIIA+TFIIE+TFIIF
+Supramolecule #4: TFIIH
+Macromolecule #1: Transcription initiation factor IIF subunit alpha
+Macromolecule #2: Transcription initiation factor IIF subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #5: Transcription initiation factor IIB
+Macromolecule #6: DNA-directed RNA polymerase subunit
+Macromolecule #7: DNA-directed RNA polymerase subunit beta
+Macromolecule #8: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #10: DNA-directed RNA polymerases I,II,and III subunit RPABC2
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #13: DNA-directed RNA polymerases II subunit RPABC5
+Macromolecule #14: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #15: DNA-directed RNA polymerases II subunit RPABC4
+Macromolecule #16: BJ4_G0050160.mRNA.1.CDS.1
+Macromolecule #17: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #18: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #19: General transcription and DNA repair factor IIH
+Macromolecule #20: Tfb1
+Macromolecule #21: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #22: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #23: RNA polymerase II transcription factor B subunit 2
+Macromolecule #24: Transcription initiation factor IIE subunit beta
+Macromolecule #25: Transcription initiation factor IIA large subunit
+Macromolecule #26: Transcription initiation factor IIA subunit 2
+Macromolecule #29: TATA-box-binding protein
+Macromolecule #30: Transcription initiation factor IIE subunit alpha
+Macromolecule #27: non-template strand DNA
+Macromolecule #28: template strand DNA
+Macromolecule #31: RNA
+Macromolecule #32: ZINC ION
+Macromolecule #33: MAGNESIUM ION
+Macromolecule #34: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |