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- EMDB-34870: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -
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Open data
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Basic information
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Title | Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome | |||||||||
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![]() | Sulfolobus acidocaldarius ribosome / RIBOSOME | |||||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / ribosome biogenesis / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.72 Å | |||||||||
![]() | Wang YH / Zhou J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome. Authors: Ying-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou / ![]() Abstract: Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome ...Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 197.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 81 KB 81 KB | Display Display | ![]() |
Images | ![]() | 128 KB | ||
Filedesc metadata | ![]() | 14.6 KB | ||
Others | ![]() ![]() | 194.2 MB 194.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hl5MC ![]() 8hkuC ![]() 8hkvC ![]() 8hkxC ![]() 8hkyC ![]() 8hkzC ![]() 8hl1C ![]() 8hl2C ![]() 8hl3C ![]() 8hl4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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_34870_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34870_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Sulfolobus acidocaldarius ribosome
+Supramolecule #1: Sulfolobus acidocaldarius ribosome
+Macromolecule #1: 23S rRNA (2991-MER)
+Macromolecule #2: 16S rRNA (1493-MER)
+Macromolecule #3: 5S rRNA (122-MER)
+Macromolecule #65: tRNA (76-MER)
+Macromolecule #66: mRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
+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: DUF2280 domain-containing protein
+Macromolecule #37: Conserved protein
+Macromolecule #38: 50S ribosomal protein L47A
+Macromolecule #39: 50S ribosomal protein L1
+Macromolecule #40: 30S ribosomal protein S2
+Macromolecule #41: 30S ribosomal protein S4e
+Macromolecule #42: 30S ribosomal protein S4
+Macromolecule #43: 30S ribosomal protein S5
+Macromolecule #44: 30S ribosomal protein S6e
+Macromolecule #45: 30S ribosomal protein S8e
+Macromolecule #46: 30S ribosomal protein S8
+Macromolecule #47: 30S ribosomal protein S11
+Macromolecule #48: 30S ribosomal protein S12
+Macromolecule #49: 30S ribosomal protein S15
+Macromolecule #50: 30S ribosomal protein S17
+Macromolecule #51: 30S ribosomal protein S24e
+Macromolecule #52: 30S ribosomal protein S27e
+Macromolecule #53: 30S ribosomal protein S3Ae
+Macromolecule #54: 30S ribosomal protein S3
+Macromolecule #55: 30S ribosomal protein S7
+Macromolecule #56: 30S ribosomal protein S10
+Macromolecule #57: 30S ribosomal protein S13
+Macromolecule #58: 30S ribosomal protein S14 type Z
+Macromolecule #59: 30S ribosomal protein S17e
+Macromolecule #60: 30S ribosomal protein S19e
+Macromolecule #61: 30S ribosomal protein S19
+Macromolecule #62: 30S ribosomal protein S9
+Macromolecule #63: 30S ribosomal protein S28e
+Macromolecule #64: 30S ribosomal protein S27ae
+Macromolecule #67: UNKNOWN
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 2D array |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1557 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |