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Open data
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Basic information
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Title | Giardia Ribosome in PRE-T Hybrid State (D2) | ||||||||||||||||||||||||
![]() | Giardia Ribosome in PRE-T Hybrid State (D2) | ||||||||||||||||||||||||
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Function / homology | ![]() endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / rRNA processing ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 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 / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.25 Å | ||||||||||||||||||||||||
![]() | Majumdar S / Emmerich AG / Sanyal S | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Authors: Soneya Majumdar / Andrew Emmerich / Sascha Krakovka / Chandra Sekhar Mandava / Staffan G Svärd / Suparna Sanyal / ![]() Abstract: Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated ...Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives. | ||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 446.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 88.2 KB 88.2 KB | Display Display | ![]() |
Images | ![]() | 165.3 KB | ||
Others | ![]() ![]() | 384.6 MB 384.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8btrMC ![]() 8br8C ![]() 8brmC ![]() 8bsiC ![]() 8bsjC ![]() 8btdC 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
File | ![]() | ||||||||||||||||||||
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Annotation | Giardia Ribosome in PRE-T Hybrid State (D2) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Giardia Ribosome in PRE-T Hybrid State (D2) Half 1
File | emd_16235_half_map_1.map | ||||||||||||
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Annotation | Giardia Ribosome in PRE-T Hybrid State (D2) Half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Giardia Ribosome in PRE-T Hybrid State (D2) Half 2
File | emd_16235_half_map_2.map | ||||||||||||
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Annotation | Giardia Ribosome in PRE-T Hybrid State (D2) Half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Giardia Ribosome in PRE-T Hybrid State (D2)
+Supramolecule #1: Giardia Ribosome in PRE-T Hybrid State (D2)
+Macromolecule #1: Ribosomal protein L2
+Macromolecule #2: Ribosomal protein L3
+Macromolecule #3: Ribosomal protein L4
+Macromolecule #6: Ribosomal protein L5
+Macromolecule #7: Ribosomal protein L39
+Macromolecule #8: Ribosomal protein L7
+Macromolecule #9: Ribosomal protein L7a
+Macromolecule #10: Ribosomal protein L6
+Macromolecule #11: Ribosomal protein L10
+Macromolecule #12: Ribosomal protein L11
+Macromolecule #13: Ribosomal protein L13
+Macromolecule #14: Ribosomal protein L14
+Macromolecule #15: Ribosomal protein L15
+Macromolecule #16: Ribosomal protein L13a
+Macromolecule #17: Ribosomal protein L17
+Macromolecule #18: Ribosomal protein L18
+Macromolecule #19: Ribosomal protein L19
+Macromolecule #20: Ribosomal protein L18a
+Macromolecule #21: Ribosomal protein L21
+Macromolecule #22: Ribosomal protein L22e
+Macromolecule #23: Ribosomal protein L23
+Macromolecule #24: Ribosomal protein L24
+Macromolecule #25: Ribosomal protein L23A
+Macromolecule #26: Ribosomal protein L26
+Macromolecule #27: Ribosomal protein L27
+Macromolecule #28: Ribosomal protein L27a
+Macromolecule #29: Ribosomal protein L29
+Macromolecule #30: Ribosomal protein L30
+Macromolecule #31: Ribosomal protein L31B
+Macromolecule #32: Ribosomal protein L32
+Macromolecule #33: Ribosomal protein L35a
+Macromolecule #34: Ribosomal protein L34
+Macromolecule #35: Ribosomal protein L29
+Macromolecule #36: Ribosomal protein L36-1
+Macromolecule #37: Ribosomal protein L37
+Macromolecule #38: Ribosomal protein L38e
+Macromolecule #39: Ribosomal protein L10a
+Macromolecule #40: Ribosomal protein L41
+Macromolecule #41: Ribosomal protein L44
+Macromolecule #42: Ribosomal protein L37a
+Macromolecule #43: Ubiquitin/Ribosomal protein L40e
+Macromolecule #45: Ribosomal protein SA
+Macromolecule #46: Ribosomal protein S2
+Macromolecule #47: Ribosomal protein S3
+Macromolecule #48: Ribosomal protein S3a
+Macromolecule #49: Ribosomal protein S4
+Macromolecule #50: Ribosomal protein S5
+Macromolecule #51: Ribosomal protein S6
+Macromolecule #52: Ribosomal protein S7
+Macromolecule #53: Ribosomal protein S8
+Macromolecule #54: Ribosomal protein S15A
+Macromolecule #55: Ribosomal protein S9
+Macromolecule #56: Ribosomal protein S10B
+Macromolecule #57: Ribosomal protein S11
+Macromolecule #58: Ribosomal protein S23
+Macromolecule #59: Ribosomal protein S13
+Macromolecule #60: Ribosomal protein S14
+Macromolecule #61: Ribosomal protein S15
+Macromolecule #62: Ribosomal protein S16
+Macromolecule #63: Ribosomal protein S17
+Macromolecule #64: Ribosomal protein S18
+Macromolecule #65: Ribosomal protein S19e
+Macromolecule #66: Ribosomal protein S20
+Macromolecule #67: Ribosomal protein S21
+Macromolecule #68: Ribosomal protein S24
+Macromolecule #69: Ribosomal protein S25
+Macromolecule #70: Ribosomal protein S26
+Macromolecule #71: Ribosomal protein S27
+Macromolecule #72: Ribosomal protein S28
+Macromolecule #73: Ribosomal protein S29A
+Macromolecule #74: Ribosomal protein S30
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #44: Large Subunit rRNA
+Macromolecule #75: Small Subunit rRNA
+Macromolecule #76: tRNA
+Macromolecule #77: tRNA
+Macromolecule #78: mRNA
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31100 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |