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Open data
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Basic information
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Title | Structure of the mammalian Pol II-SPT6 complex (composite map) | ||||||||||||
![]() | composite map for the Pol II-SPT6 model, made of the global map and the SPT6 focused map. | ||||||||||||
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![]() | Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION | ||||||||||||
Function / homology | ![]() regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / nucleosome organization / regulation of mRNA processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter ...regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / nucleosome organization / regulation of mRNA processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / 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 - Major Pathway / 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 / blastocyst formation / transcription elongation-coupled chromatin remodeling / : / : / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / organelle membrane / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription elongation by RNA polymerase I / mRNA transport / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA polymerase II activity / nucleosome binding / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / RNA splicing / positive regulation of RNA splicing / transcription elongation factor complex / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / mRNA processing / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / histone binding / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / protein dimerization activity / hydrolase activity / nuclear speck / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / chromatin binding / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
![]() | Chen Y / Kokic G / Dienemann C / Dybkov O / Urlaub H / Cramer P | ||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structure of the transcribing RNA polymerase II-Elongin complex. Authors: Ying Chen / Goran Kokic / Christian Dienemann / Olexandr Dybkov / Henning Urlaub / Patrick Cramer / ![]() ![]() Abstract: Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to ...Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 304 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.2 KB 31.2 KB | Display Display | ![]() |
Images | ![]() | 118 KB | ||
Filedesc metadata | ![]() | 10.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 584.6 KB | Display | ![]() |
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Full document | ![]() | 584.1 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oeuMC ![]() 8oevC ![]() 8oewC ![]() 8of0C C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | composite map for the Pol II-SPT6 model, made of the global map and the SPT6 focused map. | ||||||||||||||||||||||||||||||||||||
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
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Sample components
+Entire : The Pol II-SPT6 transcription elongation complex
+Supramolecule #1: The Pol II-SPT6 transcription elongation complex
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #16: Transcription elongation factor SPT6
+Macromolecule #13: Non-template DNA
+Macromolecule #15: Template DNA
+Macromolecule #14: RNA
+Macromolecule #17: MAGNESIUM ION
+Macromolecule #18: ZINC 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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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.1 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.09 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.5 µm / Nominal defocus min: 0.35000000000000003 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174029 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-8oeu: |