8G4S

40S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome with Emetine bound in V2 conformation with mRNA and three tRNAs.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 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

  • DOI: https://doi.org/10.1016/j.str.2023.12.015
  • Primary Citation of Related Structures:  
    8FRU, 8FVY, 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 intestinalis 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 intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BS79 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S2D [auth C]242Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BMZ1 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3E [auth D]217Giardia intestinalis 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 intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S7P (Fragment)G [auth F]190Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6H [auth G]248Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B6L8 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7I [auth H]201Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8J [auth I]174Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B252 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9K [auth J]189Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BKS8 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10BL [auth K]134Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BRX3 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S17PM [auth L]199Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for V6TF82 (Giardia intestinalis)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13154Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14145Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for E2RU83 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15145Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16158Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BKC6 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17137Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S18154Giardia intestinalis 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 intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for V6TE85 (Giardia intestinalis)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S20126Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B4G0 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2189Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B484 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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UniProt GroupA8B484
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S8P (Fragment)130Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for V6TFI0 (Giardia intestinalis)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S12P143Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for V6T9I6 (Giardia intestinalis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S24132Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B593 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2588Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8B8H7 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26AA [auth a]109Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BQZ7 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27BA [auth b]124Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28CA [auth c]64Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29ADA [auth d]137Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aEA [auth f]137Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S12GA [auth M]125Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BUG8 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth e]69Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A0A644F843 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,451Giardia intestinalis assemblage A
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Entity ID: 32
MoleculeChains LengthOrganismImage
E-site tRNAFA [auth g]74Giardia intestinalis assemblage A
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Entity ID: 35
MoleculeChains LengthOrganismImage
P-site tRNAIA [auth h]76Giardia intestinalis assemblage A
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Entity ID: 36
MoleculeChains LengthOrganismImage
A-site tRNAJA [auth i]75Giardia intestinalis assemblage A
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Entity ID: 37
MoleculeChains LengthOrganismImage
mRNAKA [auth k]9Giardia intestinalis 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 
LA [auth 2]emetine
C29 H40 N2 O4
AUVVAXYIELKVAI-CKBKHPSWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
IB [auth a]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],
FB [auth 2],
GB [auth 2],
HB [auth 2],
JB [auth a],
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: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

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: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references