8G4I | pdb_00008g4i

40S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome with Emetine bound in V1 conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function.

Eiler, D.R.Wimberly, B.T.Bilodeau, D.Y.Taliaferro, J.M.Reigan, P.Rissland, O.S.Kieft, J.S.

(2024) Structure 32: 400-410.e4

  • DOI: https://doi.org/10.1016/j.str.2023.12.015
  • Primary Citation of Related Structures:  
    8FRU, 8FVY, 8G4I, 8G4S

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A]245Giardia duodenalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BE86 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]248Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S2D [auth C]242Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3E [auth D]217Giardia duodenalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B8Z2 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4F [auth E]268Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S7P (Fragment)G [auth F]190Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6H [auth G]248Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7I [auth H]201Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8J [auth I]174Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9K [auth J]189Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10BL [auth K]134Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S17PM [auth L]199Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13154Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14145Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15145Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16158Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17137Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S18154Giardia duodenalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BZ58 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S19E (Fragment)158Giardia duodenalis assemblage AMutation(s): 0 
UniProt
Find proteins for A0A644F964 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20126Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2189Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S8P (Fragment)130Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S12P143Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S24132Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2588Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26AA [auth a]109Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27BA [auth b]124Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28CA [auth c]64Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29ADA [auth d]137Giardia duodenalis assemblage AMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aEA [auth f]137Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S12GA [auth M]125Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth e]69Giardia duodenalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,451Giardia duodenalis assemblage A
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Entity ID: 32
MoleculeChains LengthOrganismImage
tRNAFA [auth g]74Giardia duodenalis assemblage A
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YAT (Subject of Investigation/LOI)
Query on YAT

Download Ideal Coordinates CCD File 
IA [auth 2]emetine
C29 H40 N2 O4
AUVVAXYIELKVAI-CKBKHPSWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FB [auth a],
HB [auth d]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
BB [auth 2]
CB [auth 2]
DB [auth 2]
EB [auth 2]
AB [auth 2],
BB [auth 2],
CB [auth 2],
DB [auth 2],
EB [auth 2],
GB [auth a],
JA [auth 2],
KA [auth 2],
LA [auth 2],
MA [auth 2],
NA [auth 2],
OA [auth 2],
PA [auth 2],
QA [auth 2],
RA [auth 2],
SA [auth 2],
TA [auth 2],
UA [auth 2],
VA [auth 2],
WA [auth 2],
XA [auth 2],
YA [auth 2],
ZA [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118070
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI149210
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128680

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection