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Yorodumi- EMDB-17924: Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-Co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17924 | |||||||||
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Title | Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine | |||||||||
Map data | deepEMhancer sharpened map | |||||||||
Sample |
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Keywords | Elongator / tRNA modification / acetyl-CoA hydrolysis / TRANSLATION | |||||||||
Function / homology | Function and homology information phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development ...phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development / transcription elongation by RNA polymerase II / neuron migration / : / regulation of translation / 4 iron, 4 sulfur cluster binding / HATs acetylate histones / tRNA binding / positive regulation of cell migration / nucleolus / regulation of transcription by RNA polymerase II / protein kinase binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Abbassi N / Jaciuk M / Lin T-Y / Glatt S | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human Elp123 in complex with tRNA, acetyl-CoA, 5'-deoxyadenosine and methionine Authors: Abbassi N / Jaciuk M / Lin T-Y / Glatt S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17924.map.gz | 352.9 MB | EMDB map data format | |
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Header (meta data) | emd-17924-v30.xml emd-17924.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17924_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_17924.png | 104.6 KB | ||
Masks | emd_17924_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-17924.cif.gz | 8.7 KB | ||
Others | emd_17924_half_map_1.map.gz emd_17924_half_map_2.map.gz | 392 MB 392 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17924 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17924 | HTTPS FTP |
-Related structure data
Related structure data | 8ptxMC M: atomic model generated by this map C: citing same article (ref.) |
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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_17924.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | deepEMhancer sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17924_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17924_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17924_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxy...
+Supramolecule #1: Human Elp123 in complex with glutamine tRNA, acetyl-CoA, 5'-deoxy...
+Macromolecule #1: Elongator complex protein 1
+Macromolecule #2: Elongator complex protein 2
+Macromolecule #3: Elongator complex protein 3
+Macromolecule #4: tRNA Gln
+Macromolecule #5: IRON/SULFUR CLUSTER
+Macromolecule #6: 5'-DEOXYADENOSINE
+Macromolecule #7: ACETYL COENZYME *A
+Macromolecule #8: METHIONINE
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 8 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 15 s wait time, blot force 5, 5 s blot time. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4214 / Average electron dose: 40.09 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-8ptx: |