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Yorodumi- EMDB-34860: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34860 | |||||||||
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Title | Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Sulfolobus acidocaldarius ribosome small subunit / RIBOSOME | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / 5S rRNA binding / cytosolic large ribosomal subunit ...translation release factor activity, codon specific / ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Sulfolobus acidocaldarius DSM 639 (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Wang YH / Zhou J | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome Authors: Wang YH / Zhou J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34860.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-34860-v30.xml emd-34860.xml | 52.5 KB 52.5 KB | Display Display | EMDB header |
Images | emd_34860.png | 162.5 KB | ||
Others | emd_34860_half_map_1.map.gz emd_34860_half_map_2.map.gz | 165.1 MB 165.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34860 | HTTPS FTP |
-Related structure data
Related structure data | 8hkuMC 8hkvC 8hkxC 8hkyC 8hl4C 8hl5C 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_34860.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34860_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34860_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Sulfolobus acidocaldarius ribosome small sbunit
+Supramolecule #1: Sulfolobus acidocaldarius ribosome small sbunit
+Macromolecule #1: 23s rRNA (2996-MER)
+Macromolecule #2: 5s rRNA (122-MER)
+Macromolecule #40: E-site tRNA
+Macromolecule #3: 50S ribosomal protein L1
+Macromolecule #4: 50S ribosomal protein L2
+Macromolecule #5: 50S ribosomal protein L3
+Macromolecule #6: 50S ribosomal protein L4
+Macromolecule #7: 50S ribosomal protein L5
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L18Ae
+Macromolecule #10: 50S ribosomal protein L10e
+Macromolecule #11: 50S ribosomal protein L13
+Macromolecule #12: 50S ribosomal protein L14e
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15e
+Macromolecule #15: 50S ribosomal protein L18e
+Macromolecule #16: 50S ribosomal protein L18
+Macromolecule #17: 50S ribosomal protein L19e
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24e
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 50S ribosomal protein L29
+Macromolecule #23: 50S ribosomal protein L30e
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L31e
+Macromolecule #26: 50S ribosomal protein L32e
+Macromolecule #27: 50S ribosomal protein L34e
+Macromolecule #28: 50S ribosomal protein L37Ae
+Macromolecule #29: 50S ribosomal protein L37e
+Macromolecule #30: 50S ribosomal protein L39e
+Macromolecule #31: 50S ribosomal protein L40E
+Macromolecule #32: 50S ribosomal protein L44e
+Macromolecule #33: 50S ribosomal protein L7Ae
+Macromolecule #34: 50S ribosomal protein L15
+Macromolecule #35: 50S ribosomal protein L21e
+Macromolecule #36: Peptide chain release factor subunit 1
+Macromolecule #37: DUF2280 domain-containing protein
+Macromolecule #38: Conserved protein
+Macromolecule #39: 50S ribosomal protein L47A
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-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: 3.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 772574 |