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Yorodumi- EMDB-0673: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0673 | ||||||||||||||||||
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Title | RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) | ||||||||||||||||||
Map data | overall reconstruction (before postprocessing) | ||||||||||||||||||
Sample |
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Keywords | nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | ||||||||||||||||||
Function / homology | Function and homology information regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation ...regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / 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 / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / RNA polymerase I activity / heterochromatin organization / Packaging Of Telomere Ends / RNA polymerase II activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / translation initiation factor binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / transcription elongation factor complex / PRC2 methylates histones and DNA / innate immune response in mucosa / regulation of DNA-templated transcription elongation / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / transcription initiation at RNA polymerase II promoter / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis Similarity search - Function | ||||||||||||||||||
Biological species | Komagataella phaffii (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) / Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (fungus) / Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||||||||
Authors | Ehara H / Kujirai T | ||||||||||||||||||
Funding support | Japan, 5 items
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Citation | Journal: Science / Year: 2019 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0673.map.gz | 40.9 MB | EMDB map data format | |
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Header (meta data) | emd-0673-v30.xml emd-0673.xml | 43.6 KB 43.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0673_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_0673.png | 129.5 KB | ||
Filedesc metadata | emd-0673.cif.gz | 11.8 KB | ||
Others | emd_0673_additional_1.map.gz emd_0673_additional_2.map.gz | 47.6 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0673 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0673 | HTTPS FTP |
-Validation report
Summary document | emd_0673_validation.pdf.gz | 578.6 KB | Display | EMDB validaton report |
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Full document | emd_0673_full_validation.pdf.gz | 578.2 KB | Display | |
Data in XML | emd_0673_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_0673_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0673 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0673 | HTTPS FTP |
-Related structure data
Related structure data | 6j4yMC 0671C 0672C 0674C 0675C 0676C 9713C 6ir9C 6j4wC 6j4xC 6j4zC 6j50C 6j51C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0673.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | overall reconstruction (before postprocessing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Nucleosome reconstruction (postprocessed)
File | emd_0673_additional_1.map | ||||||||||||
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Annotation | Nucleosome reconstruction (postprocessed) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RNAPII reconstruction
File | emd_0673_additional_2.map | ||||||||||||
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Annotation | RNAPII reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+Supramolecule #1: RNA polymerase II elongation complex bound with Elf1 and Spt4/5, ...
+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 1 homolog
+Macromolecule #17: Transcription elongation factor SPT4
+Macromolecule #18: Protein that forms a complex with Spt4p
+Macromolecule #19: Histone H3.3
+Macromolecule #20: Histone H4
+Macromolecule #21: Histone H2A type 1-B/E
+Macromolecule #22: Histone H2B type 1-J
+Macromolecule #13: RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
+Macromolecule #14: DNA (198-MER)
+Macromolecule #15: DNA (198-MER)
+Macromolecule #23: ZINC ION
+Macromolecule #24: 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 R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |