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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12449 | |||||||||||||||
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Title | RNA polymerase II-Spt4/5-nucleosome-Chd1 structure | |||||||||||||||
![]() | Map D | |||||||||||||||
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Function / homology | ![]() negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / snRNP binding / negative regulation of DNA-templated DNA replication / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex ...negative regulation of transcription elongation by RNA polymerase I / positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / snRNP binding / negative regulation of DNA-templated DNA replication / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex / regulation of chromatin organization / intracellular mRNA localization / rDNA binding / RNA polymerase I general transcription initiation factor binding / nucleosome organization / SLIK (SAGA-like) complex / RPB4-RPB7 complex / U4 snRNA binding / sister chromatid cohesion / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of DNA-templated transcription, elongation / ATP-dependent chromatin remodeler activity / SAGA complex / RNA Polymerase I Transcription Initiation / transcription elongation-coupled chromatin remodeling / 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 / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / spliceosomal complex assembly / RNA polymerase II complex binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / chromosome, centromeric region / Dual incision in TC-NER / transcription elongation by RNA polymerase I / U5 snRNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / U2 snRNA binding / tRNA transcription by RNA polymerase III / U6 snRNA binding / positive regulation of autophagy / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / U1 snRNA binding / translation initiation factor binding / methylated histone binding / helicase activity / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / P-body / chromatin DNA binding / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / structural constituent of chromatin / peroxisome / nucleosome / nucleosome assembly / ribosome biogenesis / chromosome / single-stranded DNA binding / histone binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
![]() | Farnung L / Ochmann M / Engeholm M / Cramer P | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structural basis of nucleosome transcription mediated by Chd1 and FACT. Authors: Lucas Farnung / Moritz Ochmann / Maik Engeholm / Patrick Cramer / ![]() Abstract: Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is ...Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 220.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.4 KB 37.4 KB | Display Display | ![]() |
Images | ![]() | 93.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 244.9 KB | Display | ![]() |
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Full document | ![]() | 244 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nkxMC ![]() 7nkyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Map D | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : RNA polymerase II-Spt4/5-Chd1-nucleosome
+Supramolecule #1: RNA polymerase II-Spt4/5-Chd1-nucleosome
+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 polymerases I, II, and III subunit RPABC1
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #11: Histone H3.2
+Macromolecule #12: Histone H4
+Macromolecule #13: Histone H2A type 1
+Macromolecule #14: Histone H2B 1.1
+Macromolecule #17: Chromo domain-containing protein 1
+Macromolecule #19: Chromatin elongation factor SPT4
+Macromolecule #20: Transcription elongation factor SPT5
+Macromolecule #21: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #22: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #15: DNA (139-MER)
+Macromolecule #16: DNA (128-MER)
+Macromolecule #18: RNA
+Macromolecule #23: ZINC ION
+Macromolecule #24: MAGNESIUM ION
+Macromolecule #25: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #26: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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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: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30876 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |