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Yorodumi- EMDB-12968: Structure of active transcription elongation complex Pol II-DSIF-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12968 | |||||||||||||||
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Title | Structure of active transcription elongation complex Pol II-DSIF-ELL2-EAF1, Map 7, Focused map for Pol II core | |||||||||||||||
Map data | Focused map for Pol II core region (map7), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model) | |||||||||||||||
Sample |
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Function / homology | Function and homology information super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / intercellular bridge / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / : / : / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / organelle membrane / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / cis-regulatory region sequence-specific DNA binding / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / RNA polymerase II activity / Formation of RNA Pol II elongation complex / Cajal body / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / 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 / P-body / 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 / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / nuclear body / protein dimerization activity / hydrolase activity / nuclear speck / protein heterodimerization activity / RNA-directed RNA polymerase Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / HIV whole-genome vector AA1305#18 (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Chen Y / Vos SM / Dienemann C / Ninov M / Urlaub H / Cramer P | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Allosteric transcription stimulation by RNA polymerase II super elongation complex. Authors: Ying Chen / Seychelle M Vos / Christian Dienemann / Momchil Ninov / Henning Urlaub / Patrick Cramer / Abstract: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we ...The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12968.map.gz | 95.3 MB | EMDB map data format | |
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Header (meta data) | emd-12968-v30.xml emd-12968.xml | 38.3 KB 38.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12968_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_12968.png | 115.4 KB | ||
Masks | emd_12968_msk_1.map | 103 MB | Mask map | |
Others | emd_12968_half_map_1.map.gz emd_12968_half_map_2.map.gz | 80.6 MB 80.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12968 | HTTPS FTP |
-Validation report
Summary document | emd_12968_validation.pdf.gz | 470.1 KB | Display | EMDB validaton report |
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Full document | emd_12968_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | emd_12968_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_12968_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12968 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12968.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Focused map for Pol II core region (map7), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12968_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1 for the focused map of Pol II map7 (EC core)
File | emd_12968_half_map_1.map | ||||||||||||
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Annotation | half map 1 for the focused map of Pol II map7 (EC core) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 for the focused map of Pol II map 7(EC core)
File | emd_12968_half_map_2.map | ||||||||||||
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Annotation | half map 1 for the focused map of Pol II map 7(EC core) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Transcription elongation complex of RNA polymerase II with elonga...
+Supramolecule #1: Transcription elongation complex of RNA polymerase II with elonga...
+Supramolecule #2: DNA-directed RNA polymerase
+Supramolecule #3: Elongation factors
+Supramolecule #4: RNA
+Supramolecule #5: Elongation factors
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: RNA polymerase II subunit E
+Macromolecule #6: RNA polymerase II subunit F
+Macromolecule #7: RNA polymerase II subunit G
+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
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: RNA polymerase II elongation factor ELL2
+Macromolecule #14: ELL-associated factor 1
+Macromolecule #15: Transcription elongation factor SPT5
+Macromolecule #16: Transcription elongation factor SPT4
+Macromolecule #17: Template DNA
+Macromolecule #18: Non-template DNA
+Macromolecule #19: RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 43.21 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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