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Yorodumi- EMDB-6747: RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6747 | |||||||||
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Title | RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS | |||||||||
Map data | consensus map after sharpening | |||||||||
Sample |
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Keywords | transcription / complex / TRANSCRIPTION-RNA complex | |||||||||
Function / homology | Function and homology information : / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / transcription elongation-coupled chromatin remodeling ...: / regulation of septum digestion after cytokinesis / regulatory ncRNA-mediated heterochromatin formation / DSIF complex / nuclear DNA-directed RNA polymerase complex / transcription elongation factor activity / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / transcription elongation-coupled chromatin remodeling / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / RNA polymerase III activity / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / chromosome, centromeric region / RNA polymerase II activity / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / translation elongation factor activity / pericentric heterochromatin / RNA polymerase II, core complex / translation initiation factor binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / P-body / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Komagataella pastoris (fungus) / Komagataella phaffii (strain GS115 / ATCC 20864) (fungus) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.83 Å | |||||||||
Authors | Ehara H / Yokoyama T | |||||||||
Citation | Journal: Science / Year: 2017 Title: Structure of the complete elongation complex of RNA polymerase II with basal factors. Authors: Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine / Abstract: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we ...In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes. | |||||||||
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_6747.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-6747-v30.xml emd-6747.xml | 43.2 KB 43.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6747_fsc.xml | 6.4 KB | Display | FSC data file |
Images | emd_6747.png | 167.4 KB | ||
Filedesc metadata | emd-6747.cif.gz | 10.4 KB | ||
Others | emd_6747_additional_1.map.gz emd_6747_additional_2.map.gz emd_6747_additional_3.map.gz emd_6747_additional_4.map.gz | 16.9 MB 16.9 MB 16.9 MB 16.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6747 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6747 | HTTPS FTP |
-Related structure data
Related structure data | 5xonMC 5xogC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_6747.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | consensus map after sharpening | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.533 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: consensus map before sharpening
File | emd_6747_additional_1.map | ||||||||||||
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Annotation | consensus map before sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: class 1 before sharpening
File | emd_6747_additional_2.map | ||||||||||||
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Annotation | class 1 before sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: class 2 before sharpening
File | emd_6747_additional_3.map | ||||||||||||
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Annotation | class 2 before sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: class 3 before sharpening
File | emd_6747_additional_4.map | ||||||||||||
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Annotation | class 3 before sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
+Supramolecule #1: RNA polymerase II elongation complex bound with Spt4/5 and TFIIS
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: Spt4/5 and TFIIS
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: RNA polymerase II third largest subunit B44, part of central core
+Macromolecule #4: RNA polymerase II subunit B32
+Macromolecule #5: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
+Macromolecule #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+Macromolecule #7: RNA polymerase II subunit
+Macromolecule #8: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, ...
+Macromolecule #9: DNA-directed RNA polymerase subunit
+Macromolecule #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+Macromolecule #11: RNA polymerase II subunit B12.5
+Macromolecule #12: RNA polymerase subunit, found in RNA polymerase complexes I, II, ...
+Macromolecule #16: General transcription elongation factor TFIIS
+Macromolecule #17: Transcription elongation factor SPT4
+Macromolecule #18: Protein that forms a complex with Spt4p
+Macromolecule #13: RNA (30-MER)
+Macromolecule #14: DNA (48-MER)
+Macromolecule #15: DNA (48-MER)
+Macromolecule #19: ZINC ION
+Macromolecule #20: MAGNESIUM 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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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3607 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | Model fitting was done with Chimera and Coot. Well-ordered regions were also refined with phenix.real_space_refine. |
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Output model | PDB-5xon: |