+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8239 | |||||||||
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Title | EM map of the intact yeast Elongator complex | |||||||||
Map data | Endogenously purified yeast Elongator complex | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.2 Å | |||||||||
Authors | Setiaputra D / Cheng DTH / Hansen JM / Yip CK | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: EMBO Rep / Year: 2017 Title: Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement. Authors: Dheva T Setiaputra / Derrick Th Cheng / Shan Lu / Jesse M Hansen / Udit Dalwadi / Cindy Hy Lam / Jeffrey L To / Meng-Qiu Dong / Calvin K Yip / Abstract: Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique ...Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique subunits (Elp1 to Elp6). Despite the wealth of structural data on the individual subunits, the overall architecture and subunit organization of the full Elongator and the molecular mechanisms of how it exerts its multiple activities remain unclear. Using single-particle electron microscopy (EM), we revealed that yeast Elongator adopts a bilobal architecture and an unexpected asymmetric subunit arrangement resulting from the hexameric Elp456 subassembly anchored to one of the two Elp123 lobes that form the structural scaffold. By integrating the EM data with available subunit crystal structures and restraints generated from cross-linking coupled to mass spectrometry, we constructed a multiscale molecular model that showed the two Elp3, the main catalytic subunit, are located in two distinct environments. This work provides the first structural insights into Elongator and a framework to understand the molecular basis of its multifunctionality. | |||||||||
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_8239.map.gz | 714.3 KB | EMDB map data format | |
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Header (meta data) | emd-8239-v30.xml emd-8239.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8239_fsc.xml | 2.6 KB | Display | FSC data file |
Images | emd_8239.png | 74.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8239 | HTTPS FTP |
-Validation report
Summary document | emd_8239_validation.pdf.gz | 427.7 KB | Display | EMDB validaton report |
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Full document | emd_8239_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | emd_8239_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_8239_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8239 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8239 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8239.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Endogenously purified yeast Elongator complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Intact yeast Elongator complex
Entire | Name: Intact yeast Elongator complex |
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Components |
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-Supramolecule #1: Intact yeast Elongator complex
Supramolecule | Name: Intact yeast Elongator complex / type: complex / ID: 1 / Parent: 0 / Details: Endogenously purified yeast Elongator complex |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ1991 |
Molecular weight | Theoretical: 850 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: The final purification buffer was part of a glycerol gradient containing crosslinker as per the GraFix technique (Stark 2010): 40 mM HEPES, pH 7.4, 150 mM NaCl, 0.1% Tween-20, 1 mM EDTA, ...Details: The final purification buffer was part of a glycerol gradient containing crosslinker as per the GraFix technique (Stark 2010): 40 mM HEPES, pH 7.4, 150 mM NaCl, 0.1% Tween-20, 1 mM EDTA, ~20% glycerol, ~0.02% glutaraldehyde. Fractions containing the sample were concentrated and the buffer was exchanged for the final buffer: 40 mM HEPES, pH 7.4, 150 mM NaCl, 1 mM EDTA. | ||||||||||||
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Staining | Type: NEGATIVE / Material: Uranyl formate Details: Sample was applied to a glow-discharged copper grid overlaid with carbon (carbon evaporator and amyl acetate) and stained with uranyl formate. | ||||||||||||
Grid | Model: Ted Pella Gilder Grids / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 100 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 49000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |