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Yorodumi- EMDB-16610: Yeast RNA polymerase II transcription pre-initiation complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16610 | |||||||||
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Title | Yeast RNA polymerase II transcription pre-initiation complex with core Mediator | |||||||||
Map data | local resolution filtered map of raw reconstruction | |||||||||
Sample |
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Keywords | PIC / Mediator / TF / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription factor TFIIF complex / DNA 5'-3' helicase / transcription factor TFIIA complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA 3'-5' helicase / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / 3'-5' DNA helicase activity / 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 / RNA polymerase II general transcription initiation factor activity / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / nuclear-transcribed mRNA catabolic process / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / translesion synthesis / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / DNA helicase activity / TBP-class protein binding / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / 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 / peroxisome / ribosome biogenesis / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Synthetic construct (others) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wang H / Schilbach S / Cramer P | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. Authors: Sandra Schilbach / Haibo Wang / Christian Dienemann / Patrick Cramer / Abstract: For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator ...For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator structure have been reported, structures for its yeast counterpart remain incomplete. Here, we present an atomic model for the yeast PIC with core Mediator, including the Mediator middle module that was previously poorly resolved and including subunit Med1 that was previously lacking. We observe three peptide regions containing eleven of the 26 heptapeptide repeats of the flexible C-terminal repeat domain (CTD) of Pol II. Two of these CTD regions bind between the Mediator head and middle modules and form defined CTD-Mediator interactions. CTD peptide 1 binds between the Med6 shoulder and Med31 knob domains, whereas CTD peptide 2 forms additional contacts with Med4. The third CTD region (peptide 3) binds in the Mediator cradle and associates with the Mediator hook. Comparisons with the human PIC-Mediator structure show that the central region in peptide 1 is similar and forms conserved contacts with Mediator, whereas peptides 2 and 3 exhibit distinct structures and Mediator interactions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16610.map.gz | 143.2 MB | EMDB map data format | |
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Header (meta data) | emd-16610-v30.xml emd-16610.xml | 93.3 KB 93.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16610_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_16610.png | 195.4 KB | ||
Filedesc metadata | emd-16610.cif.gz | 19 KB | ||
Others | emd_16610_additional_1.map.gz emd_16610_additional_2.map.gz emd_16610_additional_3.map.gz emd_16610_additional_4.map.gz emd_16610_additional_5.map.gz emd_16610_half_map_1.map.gz emd_16610_half_map_2.map.gz | 150.2 MB 219.8 MB 214.8 MB 215.1 MB 193.1 MB 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16610 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16610 | HTTPS FTP |
-Validation report
Summary document | emd_16610_validation.pdf.gz | 837.1 KB | Display | EMDB validaton report |
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Full document | emd_16610_full_validation.pdf.gz | 836.6 KB | Display | |
Data in XML | emd_16610_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_16610_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16610 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16610 | HTTPS FTP |
-Related structure data
Related structure data | 8cenMC 8ceoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16610.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local resolution filtered map of raw reconstruction | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: composite map for model building
File | emd_16610_additional_1.map | ||||||||||||
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Annotation | composite map for model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused refinement map of cPIC
File | emd_16610_additional_2.map | ||||||||||||
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Annotation | focused refinement map of cPIC | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused refinement map of TFIIH
File | emd_16610_additional_3.map | ||||||||||||
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Annotation | focused refinement map of TFIIH | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused refinement map of cMed
File | emd_16610_additional_4.map | ||||||||||||
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Annotation | focused refinement map of cMed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: focused refinement map of cMed-CTD
File | emd_16610_additional_5.map | ||||||||||||
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Annotation | focused refinement map of cMed-CTD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_16610_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_16610_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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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...
+Supramolecule #2: DNA-directed RNA polymerase subunits
+Supramolecule #3: General transcription and DNA repair factors, and RNA polymerase ...
+Supramolecule #4: DNA
+Supramolecule #5: Transcription initiation factors and Mediator of RNA polymerase I...
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #3: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #4: RNA polymerase II transcription factor B subunit 3
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #21: Transcription initiation factor IIB
+Macromolecule #23: TATA-binding protein
+Macromolecule #24: Transcription initiation factor IIF subunit alpha
+Macromolecule #25: Transcription initiation factor IIF subunit beta
+Macromolecule #27: Transcription initiation factor IIA large subunit
+Macromolecule #28: Transcription initiation factor IIA subunit 2
+Macromolecule #29: Transcription initiation factor IIE subunit alpha
+Macromolecule #30: Transcription initiation factor IIE subunit beta
+Macromolecule #31: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #32: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #33: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #34: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #35: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #36: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #37: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #38: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #42: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #43: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 1
+Macromolecule #22: NONTEMPLATE DNA (209-MER)
+Macromolecule #26: TEMPLATE DNA (209-MER)
+Macromolecule #47: IRON/SULFUR CLUSTER
+Macromolecule #48: ZINC ION
+Macromolecule #49: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 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 |