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- EMDB-0674: RNA polymerase II elongation complex bound with Spt4/5 and foreig... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0674 | |||||||||||||||||||||
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Title | RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome | |||||||||||||||||||||
![]() | Overall reconstruction (before postprocess) | |||||||||||||||||||||
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![]() | nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||||||||||||||
Function / homology | ![]() regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / negative regulation of chromosome condensation / DSIF complex / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / RPB4-RPB7 complex / pericentric heterochromatin formation / inner kinetochore / transcription elongation factor activity / oocyte maturation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / chromosome, centromeric region / RNA polymerase II activity / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / transcription elongation by RNA polymerase I / single fertilization / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / negative regulation of megakaryocyte differentiation / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / translation initiation factor binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / regulation of DNA-templated transcription elongation / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / P-body / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / ribonucleoside binding / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||||||||
![]() | Ehara H / Kujirai T | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Authors: Haruhiko Ehara / Tomoya Kujirai / Yuka Fujino / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine / ![]() Abstract: RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional ...RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions. | |||||||||||||||||||||
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 | ![]() | 40.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 43.9 KB 43.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 121.1 KB | ||
Filedesc metadata | ![]() | 11.7 KB | ||
Others | ![]() ![]() | 40.7 MB 48.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j4zMC ![]() 0671C ![]() 0672C ![]() 0673C ![]() 0675C ![]() 0676C ![]() 9713C ![]() 6ir9C ![]() 6j4wC ![]() 6j4xC ![]() 6j4yC ![]() 6j50C ![]() 6j51C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Overall reconstruction (before postprocess) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: RNAP reconstruction
File | emd_0674_additional_1.map | ||||||||||||
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Annotation | RNAP reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nucleosome reconstruction (postprocessed)
File | emd_0674_additional_2.map | ||||||||||||
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Annotation | Nucleosome reconstruction (postprocessed) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : RNA polymerase II elongation complex bound with Spt4/5 and foreig...
+Supramolecule #1: RNA polymerase II elongation complex bound with Spt4/5 and foreig...
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: RNA polymerase II third largest subunit B44, part of central core
+Macromolecule #4: RNA polymerase II subunit B32
+Macromolecule #5: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
+Macromolecule #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+Macromolecule #7: RNA polymerase II subunit
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase subunit
+Macromolecule #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+Macromolecule #11: RNA polymerase II subunit B12.5
+Macromolecule #12: RNA polymerase subunit ABC10-alpha
+Macromolecule #16: Transcription elongation factor SPT4
+Macromolecule #17: Spt5
+Macromolecule #18: Histone H3.3
+Macromolecule #19: Histone H4
+Macromolecule #20: Histone H2A type 1-B/E
+Macromolecule #21: Histone H2B type 1-J
+Macromolecule #13: RNA (5'-R(P*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')
+Macromolecule #14: DNA (198-MER)
+Macromolecule #15: DNA (198-MER)
+Macromolecule #22: DNA (42-MER)
+Macromolecule #23: DNA (42-MER)
+Macromolecule #24: ZINC ION
+Macromolecule #25: MAGNESIUM 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |