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Yorodumi- EMDB-16830: Structure of the mammalian Pol II-Elongin complex, lacking ELOA l... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16830 | ||||||||||||
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Title | Structure of the mammalian Pol II-Elongin complex, lacking ELOA latch (Focused map for elongin, map 5) | ||||||||||||
Map data | map 5(postprocess map). Focused map for Elongin in the composite map for the Pol II-Elongin (NoN) high resolution model | ||||||||||||
Sample |
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Keywords | Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 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_16830.map.gz | 300.1 MB | EMDB map data format | |
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Header (meta data) | emd-16830-v30.xml emd-16830.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16830_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_16830.png | 74.2 KB | ||
Masks | emd_16830_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-16830.cif.gz | 4.3 KB | ||
Others | emd_16830_half_map_1.map.gz emd_16830_half_map_2.map.gz | 260.1 MB 260.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16830 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16830 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16830.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | map 5(postprocess map). Focused map for Elongin in the composite map for the Pol II-Elongin (NoN) high resolution model | ||||||||||||||||||||
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
File | emd_16830_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map1 of map 5
File | emd_16830_half_map_1.map | ||||||||||||
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Annotation | half map1 of map 5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map2 of map 5
File | emd_16830_half_map_2.map | ||||||||||||
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Annotation | half map2 of map 5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The Pol II-SPT6-Elongin transcription elongation complex
Entire | Name: The Pol II-SPT6-Elongin transcription elongation complex |
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Components |
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-Supramolecule #1: The Pol II-SPT6-Elongin transcription elongation complex
Supramolecule | Name: The Pol II-SPT6-Elongin transcription elongation complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18 Details: The map is generated from a sub-class of a cryo-EM dataset for the Pol II-SPT6-Elongin complex. |
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Source (natural) | Organism: Homo sapiens (human) |
-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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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