+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16835 | ||||||||||||
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Title | Structure of the mammalian Pol II-SPT6 complex (composite map) | ||||||||||||
Map data | composite map for the Pol II-SPT6 model, made of the global map and the SPT6 focused map. | ||||||||||||
Sample |
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Keywords | Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information 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 / blastocyst formation / 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 / transcription elongation-coupled chromatin remodeling / : / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II activity / organelle membrane / nucleosome binding / transcription-coupled nucleotide-excision repair / mRNA transport / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of RNA splicing / transcription elongation factor complex / DNA-directed RNA polymerase complex / RNA splicing / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / fibrillar center / mRNA processing / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / nucleic acid binding / protein dimerization activity / nuclear speck / RNA-directed RNA polymerase / nucleotide binding / DNA-templated transcription / chromatin binding / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
Authors | Chen Y / Kokic G / Dienemann C / Dybkov O / Urlaub H / Cramer P | ||||||||||||
Funding support | European Union, Germany, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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 | emd_16835.map.gz | 304 MB | EMDB map data format | |
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Header (meta data) | emd-16835-v30.xml emd-16835.xml | 31.2 KB 31.2 KB | Display Display | EMDB header |
Images | emd_16835.png | 118 KB | ||
Filedesc metadata | emd-16835.cif.gz | 10.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16835 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16835 | HTTPS FTP |
-Related structure data
Related structure data | 8oeuMC 8oevC 8oewC 8of0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16835.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.5 µm / Nominal defocus min: 0.35000000000000003 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.09 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174029 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8oeu: |