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Yorodumi- EMDB-16335: RNA polymerase II core pre-initiation complex with the proximal +... -
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-Basic information
Entry | Database: EMDB / ID: EMD-16335 | |||||||||
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Title | RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Abortive And Retractive Initiation / nuclear lumen / transcription factor TFIIA complex / : / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / cell division site / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / protein acetylation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / viral transcription / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of translational initiation / RNA polymerase II activity / organelle membrane / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Xenopus laevis (African clawed frog) / unidentified adenovirus / Homo sapiens (human) / pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Abril-Garrido J / Dienemann C / Grabbe F / Velychko T / Lidschreiber M / Wang H / Cramer P | |||||||||
Funding support | Germany, European Union, 2 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Authors: Julio Abril-Garrido / Christian Dienemann / Frauke Grabbe / Taras Velychko / Michael Lidschreiber / Haibo Wang / Patrick Cramer / Abstract: At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further ...At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16335.map.gz | 217.4 MB | EMDB map data format | |
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Header (meta data) | emd-16335-v30.xml emd-16335.xml | 52 KB 52 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16335_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_16335.png | 70.4 KB | ||
Masks | emd_16335_msk_1.map | 244.1 MB | Mask map | |
Others | emd_16335_half_map_1.map.gz emd_16335_half_map_2.map.gz | 192.2 MB 192.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16335 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16335 | HTTPS FTP |
-Related structure data
Related structure data | 8bz1MC 8bvwC 8byqC C: citing same article (ref.) M: atomic model generated by this map |
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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_16335.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Mask #1
File | emd_16335_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16335_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16335_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II core pre-initiation complex with the proximal +...
+Supramolecule #1: RNA polymerase II core pre-initiation complex with the proximal +...
+Supramolecule #2: Mammalian RNA polymerase II
+Supramolecule #3: Nucleosome (protein)
+Supramolecule #4: Nucleosome (DNA)
+Supramolecule #5: General transcription factor IIB
+Supramolecule #6: TATA-box binding protein
+Supramolecule #7: General transcription factor IIF
+Supramolecule #8: General transcription factor IIA
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+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-a
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #15: TATA-box-binding protein
+Macromolecule #16: General transcription factor IIF subunit 1
+Macromolecule #17: General transcription factor IIF subunit 2
+Macromolecule #19: Transcription initiation factor IIA subunit 1
+Macromolecule #20: Transcription initiation factor IIA subunit 2
+Macromolecule #21: Histone H3.2
+Macromolecule #22: Histone H4
+Macromolecule #23: Histone H2A type 1
+Macromolecule #24: Histone H2B 1.1
+Macromolecule #14: Non-template DNA
+Macromolecule #18: Template DNA
+Macromolecule #25: ZINC ION
+Macromolecule #26: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 36478 / Average exposure time: 3.0 sec. / Average electron dose: 50.45 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8bz1: |