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Yorodumi- 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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Keywords | RNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 / TRANSCRIPTION | |||||||||
| Function / homology | Function and homology informationpeptidyl-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 / regulation of mRNA export from nucleus ...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 / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / inner cell mass cell differentiation / positive regulation of mRNA 3'-end processing / 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 / mRNA 3'-end processing / nuclear lumen / 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 / negative regulation of gene expression, epigenetic / 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 / 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 / protein localization to nucleus / positive regulation of Wnt signaling pathway / 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 fibroblast proliferation / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of megakaryocyte differentiation / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / protein localization to CENP-A containing chromatin Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 6.72 Å | |||||||||
Authors | Walshe JL / Ochmann M / Dienemann C / Cramer P | |||||||||
| Funding support | Germany, 1 items
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Citation | Journal: To Be PublishedTitle: 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 | |||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_54425.map.gz | 31.1 MB | EMDB map data format | |
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| Header (meta data) | emd-54425-v30.xml emd-54425.xml | 59.6 KB 59.6 KB | Display Display | EMDB header |
| Images | emd_54425.png | 36.6 KB | ||
| Filedesc metadata | emd-54425.cif.gz | 17.6 KB | ||
| Others | emd_54425_half_map_1.map.gz emd_54425_half_map_2.map.gz | 414.2 MB 414.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54425 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54425 | HTTPS FTP |
-Validation report
| Summary document | emd_54425_validation.pdf.gz | 829.8 KB | Display | EMDB validaton report |
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| Full document | emd_54425_full_validation.pdf.gz | 829.3 KB | Display | |
| Data in XML | emd_54425_validation.xml.gz | 18.8 KB | Display | |
| Data in CIF | emd_54425_validation.cif.gz | 22.6 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-54425 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-54425 | 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 F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_54425.map.gz / Format: CCP4 / Size: 512 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
-Half map: #2
| File | emd_54425_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_54425_half_map_2.map | ||||||||||||
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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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Processing | 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: FIELD EMISSION GUN |
| 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 |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Germany, 1 items
Citation


































Z (Sec.)
Y (Row.)
X (Col.)




































Trichoplusia ni (cabbage looper)
Processing
FIELD EMISSION GUN
