+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16339 | |||||||||
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Title | RNA polymerase II core pre-initiation complex focused map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_16339.map.gz | 79.7 MB | EMDB map data format | |
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Header (meta data) | emd-16339-v30.xml emd-16339.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16339_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_16339.png | 72.8 KB | ||
Masks | emd_16339_msk_1.map | 103 MB | Mask map | |
Others | emd_16339_additional_1.map.gz emd_16339_half_map_1.map.gz emd_16339_half_map_2.map.gz | 89.3 MB 80.3 MB 80.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16339 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16339 | HTTPS FTP |
-Validation report
Summary document | emd_16339_validation.pdf.gz | 956.6 KB | Display | EMDB validaton report |
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Full document | emd_16339_full_validation.pdf.gz | 956.1 KB | Display | |
Data in XML | emd_16339_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_16339_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16339 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16339 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16339.map.gz / Format: CCP4 / Size: 103 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_16339_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_16339_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16339_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16339_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
Entire | Name: RNA polymerase II core pre-initiation complex |
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Components |
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-Supramolecule #1: RNA polymerase II core pre-initiation complex
Supramolecule | Name: RNA polymerase II core pre-initiation complex / type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 800 KDa |
-Supramolecule #2: Mammalian RNA polymerase II
Supramolecule | Name: Mammalian RNA polymerase II / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Sus scrofa (pig) |
-Supramolecule #3: General transcription factors
Supramolecule | Name: General transcription factors / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-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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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |