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Yorodumi- EMDB-16274: RNA polymerase II pre-initiation complex with the distal +1 nucle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16274 | |||||||||
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Title | RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / 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 I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / 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 / 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 - 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / DNA 3'-5' helicase / [RNA-polymerase]-subunit kinase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spinal cord development / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Xenopus laevis (African clawed frog) / unidentified adenovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_16274.map.gz | 213.4 MB | EMDB map data format | |
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Header (meta data) | emd-16274-v30.xml emd-16274.xml | 76.8 KB 76.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16274_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_16274.png | 58.9 KB | ||
Masks | emd_16274_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-16274.cif.gz | 17.1 KB | ||
Others | emd_16274_half_map_1.map.gz emd_16274_half_map_2.map.gz | 194.7 MB 194.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16274 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16274 | HTTPS FTP |
-Validation report
Summary document | emd_16274_validation.pdf.gz | 840.8 KB | Display | EMDB validaton report |
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Full document | emd_16274_full_validation.pdf.gz | 840.4 KB | Display | |
Data in XML | emd_16274_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_16274_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16274 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16274 | HTTPS FTP |
-Related structure data
Related structure data | 8bvwMC 8byqC 8bz1C 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_16274.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_16274_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16274_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16274_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II pre-initiation complex with the distal +1 nucleosome
+Supramolecule #1: RNA polymerase II pre-initiation complex with the distal +1 nucleosome
+Supramolecule #2: General transcription factor IIH
+Supramolecule #3: Mammalian RNA polymerase II
+Supramolecule #4: Nucleosome (protein)
+Supramolecule #5: Nucleosome (DNA)
+Supramolecule #6: General transcription factor IIB
+Supramolecule #7: TATA-box binding protein
+Supramolecule #8: General transcription factor IIF
+Supramolecule #9: General transcription factor IIA
+Supramolecule #10: General transcription factor IIE
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #2: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #3: General transcription factor IIH subunit 1
+Macromolecule #4: General transcription factor IIH subunit 4
+Macromolecule #5: General transcription factor IIH subunit 2
+Macromolecule #6: General transcription factor IIH subunit 3
+Macromolecule #7: General transcription factor IIH subunit 5
+Macromolecule #8: CDK-activating kinase assembly factor MAT1
+Macromolecule #9: Cyclin-dependent kinase 7
+Macromolecule #10: Cyclin-H
+Macromolecule #11: DNA-directed RNA polymerase subunit
+Macromolecule #12: DNA-directed RNA polymerase subunit beta
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #14: RNA polymerase II subunit D
+Macromolecule #15: DNA-directed RNA polymerase II subunit E
+Macromolecule #16: DNA-directed RNA polymerase II subunit F
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #21: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #22: RNA polymerase II subunit K
+Macromolecule #23: Transcription initiation factor IIB
+Macromolecule #25: TATA-box-binding protein
+Macromolecule #26: General transcription factor IIF subunit 1
+Macromolecule #27: General transcription factor IIF subunit 2
+Macromolecule #29: Transcription initiation factor IIA subunit 1
+Macromolecule #30: Transcription initiation factor IIA subunit 2
+Macromolecule #31: General transcription factor IIE subunit 1
+Macromolecule #32: Transcription initiation factor IIE subunit beta
+Macromolecule #33: Unassigned peptide, likely XPB
+Macromolecule #34: Unassigned peptide, likely TFIIE-beta
+Macromolecule #35: Histone H3.2
+Macromolecule #36: Histone H4
+Macromolecule #37: Histone H2A type 1
+Macromolecule #38: Histone H2B 1.1
+Macromolecule #24: Non-template DNA
+Macromolecule #28: Template DNA
+Macromolecule #39: IRON/SULFUR CLUSTER
+Macromolecule #40: ZINC ION
+Macromolecule #41: 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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Specialist optics | Energy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 41517 / Average exposure time: 3.0 sec. / Average electron dose: 41.58 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: 1.5 µm / Nominal defocus min: 0.5 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8bvw: |