[English] 日本語
Yorodumi- EMDB-14928: Yeast RNA polymerase II transcription pre-initiation complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14928 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) | |||||||||
Map data | cryo-EM map of yeast PIC in complex with the 1 nucleosome | |||||||||
Sample |
| |||||||||
Keywords | PIC / nucleosome / TF / TRANSCRIPTION | |||||||||
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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III ...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 / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II core complex assembly / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA duplex unwinding / transcription preinitiation complex / DNA binding, bending / RNA Polymerase I Transcription Initiation / 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 / termination of RNA polymerase II transcription / 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 / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / 3'-5' DNA helicase activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase II activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase I activity / RNA polymerase II, core complex / translesion synthesis / 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 / cytoplasmic stress granule / mRNA processing Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Wang H / Cramer P | |||||||||
Funding support | European Union, Germany, 2 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structures of transcription preinitiation complex engaged with the +1 nucleosome. Authors: Haibo Wang / Sandra Schilbach / Momchil Ninov / Henning Urlaub / Patrick Cramer / Abstract: The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on ...The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14928.map.gz | 112 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14928-v30.xml emd-14928.xml | 65.9 KB 65.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14928_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_14928.png | 147.4 KB | ||
Filedesc metadata | emd-14928.cif.gz | 15.8 KB | ||
Others | emd_14928_additional_1.map.gz emd_14928_half_map_1.map.gz emd_14928_half_map_2.map.gz | 119.6 MB 162.4 MB 162.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14928 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14928 | HTTPS FTP |
-Related structure data
Related structure data | 7zsaMC 7zs9C 7zsbC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_14928.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cryo-EM map of yeast PIC in complex with the 1 nucleosome | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: core PIC map without post-processing shows better density...
File | emd_14928_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | core PIC map without post-processing shows better density for Rpb6 NTT. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_14928_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_14928_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Yeast RNA polymerase II transcription pre-initiation complex with...
+Supramolecule #1: Yeast RNA polymerase II transcription pre-initiation complex with...
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #15: TATA-box-binding protein
+Macromolecule #16: Transcription initiation factor IIF subunit alpha
+Macromolecule #17: Transcription initiation factor IIF subunit beta
+Macromolecule #19: Transcription initiation factor IIA large subunit
+Macromolecule #20: Transcription initiation factor IIA subunit 2
+Macromolecule #21: Transcription initiation factor IIE subunit alpha
+Macromolecule #22: Transcription initiation factor IIE subunit beta
+Macromolecule #23: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #24: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #25: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #26: RNA polymerase II transcription factor B subunit 3
+Macromolecule #27: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #28: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #29: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #30: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #31: Histone H3.2
+Macromolecule #32: Histone H4
+Macromolecule #33: Histone H2A
+Macromolecule #34: Histone H2B 1.1
+Macromolecule #14: Non-template DNA (209-MER)
+Macromolecule #18: Template DNA (209-MER)
+Macromolecule #35: ZINC ION
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil R2/2 / Material: GOLD |
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: 41.0 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |