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- EMDB-16840: Structure of the mammalian Pol II-SPT6-Elongin complex, Structure... -
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Open data
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Basic information
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Title | Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1 (local resolution filtered map) | ||||||||||||
![]() | Local resolution filtered map for structure 1, Pol II-SPT6-Elongin model with ELOA latch | ||||||||||||
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![]() | Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION | ||||||||||||
Function / homology | ![]() regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of mRNA processing / : / nucleosome organization / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...regulation of isotype switching / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / regulation of mRNA processing / : / nucleosome organization / 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 / target-directed miRNA degradation / elongin complex / VCB complex / blastocyst formation / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / transcription elongation-coupled chromatin remodeling / RNA polymerase III activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / site of DNA damage / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription elongation by RNA polymerase I / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / mRNA transport / Formation of HIV-1 elongation complex containing HIV-1 Tat / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase I activity / RNA polymerase II, core complex / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / RNA splicing / transcription corepressor binding / 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 / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / P-body / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / ribonucleoside binding / fibrillar center / Regulation of expression of SLITs and ROBOs / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA processing / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / Neddylation / protein-macromolecule adaptor activity / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / histone binding / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 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 | ![]() | 182.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 38.9 KB 38.9 KB | Display Display | ![]() |
Images | ![]() | 108.3 KB | ||
Masks | ![]() | 325 MB | ![]() | |
Filedesc metadata | ![]() | 12 KB | ||
Others | ![]() ![]() | 261.7 MB 261.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8of0MC ![]() 8oeuC ![]() 8oevC ![]() 8oewC 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 | Local resolution filtered map for structure 1, Pol II-SPT6-Elongin model with ELOA latch | ||||||||||||||||||||
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
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: half map 1 for the local resolution filtered map
File | emd_16840_half_map_1.map | ||||||||||||
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Annotation | half map 1 for the local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2 for the local resolution filtered map
File | emd_16840_half_map_2.map | ||||||||||||
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Annotation | half map 2 for the local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : The Pol II-SPT6-Elongin transcription elongation complex
+Supramolecule #1: The Pol II-SPT6-Elongin 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: Elongin-B
+Macromolecule #17: Elongin-A
+Macromolecule #18: Elongin-C
+Macromolecule #19: Transcription elongation factor SPT6
+Macromolecule #13: Non-template DNA
+Macromolecule #15: Template DNA
+Macromolecule #14: RNA
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72087 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Details | Rigid body fit |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-8of0: |