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- EMDB-54425: State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 ... -
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Basic information
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Title | State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 | |||||||||
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![]() | RNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 / TRANSCRIPTION | |||||||||
Function / homology | ![]() peptidyl-lysine trimethylation / FACT complex / blastocyst growth / microtubule cytoskeleton organization involved in mitosis / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / [histone H3]-lysine36 N-trimethyltransferase / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / positive regulation of mRNA 3'-end processing ...peptidyl-lysine trimethylation / FACT complex / blastocyst growth / microtubule cytoskeleton organization involved in mitosis / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / [histone H3]-lysine36 N-trimethyltransferase / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / positive regulation of mRNA 3'-end processing / inner cell mass cell differentiation / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / regulation of isotype switching / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of DNA-templated transcription, elongation / regulation of muscle cell differentiation / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / DSIF complex / trophectodermal cell differentiation / histone H3K36 methyltransferase activity / regulation of transcription elongation by RNA polymerase II / blastocyst hatching / response to alkaloid / nucleosome organization / response to type I interferon / 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 / blastocyst formation / protein-lysine N-methyltransferase activity / positive regulation of ossification / nuclear lumen / mRNA 3'-end processing / regulation of protein localization to chromatin / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / response to metal ion / Abortive elongation of HIV-1 transcript in the absence of Tat / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / transcription factor TFIID complex / stem cell population maintenance / interleukin-6-mediated signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription elongation-coupled chromatin remodeling / negative regulation of gene expression, epigenetic / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / endodermal cell differentiation / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of interferon-alpha production / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of Wnt signaling pathway / protein localization to nucleus / cell surface receptor signaling pathway via JAK-STAT / mRNA transport / alpha-tubulin binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / mismatch repair / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / negative regulation of megakaryocyte differentiation / negative regulation of fibroblast proliferation / Formation of HIV elongation complex in the absence of HIV Tat / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.72 Å | |||||||||
![]() | Walshe JL / Ochmann M / Dienemann C / Cramer P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of co-transcriptional H3K36 methylation by SETD2 Authors: Walshe JL / Ochmann M / Neef U / Dybkov O / Dienemann C / Oberthuer C / Zheenbekova A / Urlaub H / Cramer P | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 59.6 KB 59.6 KB | Display Display | ![]() |
Images | ![]() | 36.6 KB | ||
Filedesc metadata | ![]() | 17.6 KB | ||
Others | ![]() ![]() | 414.2 MB 414.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 829.8 KB | Display | ![]() |
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Full document | ![]() | 829.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9s0uMC ![]() 9rtnC ![]() 9rzcC ![]() 9rzdC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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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
-Half map: #2
File | emd_54425_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_54425_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : RNA Pol II activated elongation complex with SETD2 bound to dista...
+Supramolecule #1: RNA Pol II activated elongation complex with SETD2 bound to dista...
+Macromolecule #1: RNA polymerase II subunit D
+Macromolecule #2: DNA-directed RNA polymerase II subunit E
+Macromolecule #3: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #6: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #8: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #9: RNA polymerase II subunit K
+Macromolecule #11: RNA polymerase-associated protein CTR9 homolog
+Macromolecule #13: WD repeat-containing protein 61
+Macromolecule #14: Parafibromin
+Macromolecule #15: Transcription elongation factor SPT4
+Macromolecule #16: Histone H3.2
+Macromolecule #17: Histone H4
+Macromolecule #18: Histone H2A type 1-B/E
+Macromolecule #19: Histone H2B type 1-K
+Macromolecule #20: FACT complex subunit SPT16
+Macromolecule #21: DNA-directed RNA polymerase subunit
+Macromolecule #22: DNA-directed RNA polymerase subunit beta
+Macromolecule #23: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #24: Transcription elongation factor SPT6
+Macromolecule #26: Histone-lysine N-methyltransferase SETD2
+Macromolecule #27: RNA polymerase-associated protein RTF1 homolog
+Macromolecule #28: Transcription elongation factor A protein 1
+Macromolecule #29: RNA polymerase-associated protein LEO1
+Macromolecule #30: RNA polymerase II-associated factor 1 homolog
+Macromolecule #31: Transcription elongation factor SPT5
+Macromolecule #10: RNA (46-MER)
+Macromolecule #12: Template DNA
+Macromolecule #25: Non-template DNA
+Macromolecule #32: ZINC ION
+Macromolecule #33: 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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.83 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |