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- EMDB-29730: 40S ribosomal subunit of the 80S Giardia intestinalis assemblage ... -
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Open data
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Basic information
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Title | 40S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome with Emetine bound in V2 conformation with mRNA and three tRNAs. | ||||||||||||
![]() | Composite map of cryosparc_80S_A_P_tRNA_map_sharp_EMaligned.mrc and cryosparc_40S_head_A_P_tRNA_map_sharp_EMaligned.mrc | ||||||||||||
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![]() | Giardia lamblia / Ribosome structure / Translation / parasite / RIBOSOME | ||||||||||||
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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis ...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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | ||||||||||||
![]() | Eiler DR / Wimberly BT / Bilodeau DY / Rissland OS / Kieft JS | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function. Authors: Daniel R Eiler / Brian T Wimberly / Danielle Y Bilodeau / J Matthew Taliaferro / Philip Reigan / Olivia S Rissland / Jeffrey S Kieft / ![]() Abstract: Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure ...Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 320.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.1 KB 56.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 24.3 KB | Display | ![]() |
Images | ![]() | 41.9 KB | ||
Filedesc metadata | ![]() | 11.3 KB | ||
Others | ![]() ![]() ![]() ![]() | 320.5 MB 320.4 MB 1.2 GB 1.2 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g4sMC ![]() 8fruC ![]() 8fvyC 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 | Composite map of cryosparc_80S_A_P_tRNA_map_sharp_EMaligned.mrc and cryosparc_40S_head_A_P_tRNA_map_sharp_EMaligned.mrc | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8211 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Overall 80S ribosome map
File | emd_29730_additional_1.map | ||||||||||||
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Annotation | Overall 80S ribosome map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refinement of the head of the 40S ribosomal subunit.
File | emd_29730_additional_2.map | ||||||||||||
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Annotation | Focused refinement of the head of the 40S ribosomal subunit. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of cryosparc 40S head A P tRNA map sharp EMaligned.mrc
File | emd_29730_half_map_1.map | ||||||||||||
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Annotation | Half map of cryosparc_40S_head_A_P_tRNA_map_sharp_EMaligned.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of cryosparc 40S head A P tRNA map sharp EMaligned.mrc
File | emd_29730_half_map_2.map | ||||||||||||
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Annotation | Half map of cryosparc_40S_head_A_P_tRNA_map_sharp_EMaligned.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 40S ribosomal subunit of the 80S Giardia intestinalis assemblage ...
+Supramolecule #1: 40S ribosomal subunit of the 80S Giardia intestinalis assemblage ...
+Macromolecule #1: 18S rRNA
+Macromolecule #32: E-site tRNA
+Macromolecule #35: P-site tRNA
+Macromolecule #36: A-site tRNA
+Macromolecule #37: mRNA
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: Ribosomal protein S2
+Macromolecule #5: Ribosomal protein S3
+Macromolecule #6: 40S ribosomal protein S4
+Macromolecule #7: SSU ribosomal protein S7P (Fragment)
+Macromolecule #8: 40S ribosomal protein S6
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S8
+Macromolecule #11: Ribosomal protein S9
+Macromolecule #12: Ribosomal protein S10B
+Macromolecule #13: SSU ribosomal protein S17P
+Macromolecule #14: Ribosomal protein S13
+Macromolecule #15: Ribosomal protein S14
+Macromolecule #16: Ribosomal protein S15
+Macromolecule #17: Ribosomal protein S16
+Macromolecule #18: Ribosomal protein S17
+Macromolecule #19: Ribosomal protein S18
+Macromolecule #20: SSU ribosomal protein S19E (Fragment)
+Macromolecule #21: Ribosomal protein S20
+Macromolecule #22: 40S ribosomal protein S21
+Macromolecule #23: SSU ribosomal protein S8P (Fragment)
+Macromolecule #24: SSU ribosomal protein S12P
+Macromolecule #25: Ribosomal protein S24
+Macromolecule #26: 40S ribosomal protein S25
+Macromolecule #27: 40S ribosomal protein S26
+Macromolecule #28: Ribosomal protein S27
+Macromolecule #29: Ribosomal protein S28
+Macromolecule #30: Ribosomal protein S29A
+Macromolecule #31: Ribosomal protein S27a
+Macromolecule #33: Ribosomal protein S12
+Macromolecule #34: 40S ribosomal protein S30
+Macromolecule #38: emetine
+Macromolecule #39: MAGNESIUM ION
+Macromolecule #40: ZINC ION
+Macromolecule #41: water
-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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.26 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: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |