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- PDB-9s0u: State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9s0u | |||||||||||||||||||||
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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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![]() | TRANSCRIPTION / RNA Pol II Activated elongation complex Co-transcriptional H3K36me3 SETD2 | |||||||||||||||||||||
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 | ![]() ![]() ![]() synthetic construct (others) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.72 Å | |||||||||||||||||||||
![]() | Walshe, J.L. / Ochmann, M. / Dienemann, C. / Cramer, P. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of co-transcriptional H3K36 methylation by SETD2 Authors: Walshe, J.L. / Ochmann, M. / Neef, U. / Dybkov, O. / Dienemann, C. / Oberthuer, C. / Zheenbekova, A. / Urlaub, H. / Cramer, P. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 216.5 KB | Display | |
Data in CIF | ![]() | 349 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 54425MC ![]() 9rtnC ![]() 9rzcC ![]() 9rzdC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA polymerase II subunit ... , 2 types, 2 molecules DL
#1: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerase ... , 7 types, 7 molecules EGIKABC
#2: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 217610.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A8D1DPV6, DNA-directed RNA polymerase |
#22: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ
#3: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 1 types, 1 molecules P
#10: RNA chain | Mass: 14843.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-RNA polymerase-associated protein ... , 3 types, 3 molecules QRU
#11: Protein | Mass: 134510.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#27: Protein | Mass: 80733.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#29: Protein | Mass: 75514.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules TN
#12: DNA chain | Mass: 60522.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#25: DNA chain | Mass: 61155.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 9 types, 13 molecules WXaebfcgdhkOV
#13: Protein | Mass: 33617.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||||||
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#14: Protein | Mass: 60673.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||
#16: Protein | Mass: 15391.052 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D Production host: ![]() ![]() #17: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4 Production host: ![]() ![]() #18: Protein | Mass: 14721.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #19: Protein | Mass: 13921.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #20: Protein | | Mass: 120290.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #26: Protein | | Mass: 127887.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases #30: Protein | | Mass: 60052.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Transcription elongation factor ... , 4 types, 4 molecules YMSZ
#15: Protein | Mass: 13508.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#24: Protein | Mass: 199602.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#28: Protein | Mass: 34294.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#31: Protein | Mass: 121225.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 2 types, 10 molecules 


#32: Chemical | ChemComp-ZN / #33: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Type: COMPLEX / Entity ID: #1-#31 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 39.83 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 6.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21738 / Symmetry type: POINT |