8FRU

60S subunit of the Giardia lamblia 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL3A [auth B]379Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL15B [auth a]149Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL4316Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL16D [auth I]210Giardia intestinalis assemblage AMutation(s): 0 
UniProt
Find proteins for A8BM86 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL43E [auth p]94Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL18F [auth D]297Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL6G [auth H]185Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL8H [auth G]225Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL5I [auth J]173Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL13J [auth O]197Giardia intestinalis assemblage AMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL13K [auth L]234Giardia intestinalis assemblage AMutation(s): 0 
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Find proteins for A8B6M8 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL14L [auth M]131Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL15M [auth N]204Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL18N [auth Q]179Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL20O [auth S]205Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL19P [auth R]196Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL21Q [auth T]159Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL14R [auth V]142Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL22S [auth P]164Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL23T [auth X]141Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL24U [auth Y]135Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL24V [auth W]102Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL27W [auth Z]135Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL29X [auth b]62Giardia intestinalis assemblage AMutation(s): 0 
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Find proteins for V6TAA6 (Giardia intestinalis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL29Y [auth h]124Giardia intestinalis assemblage AMutation(s): 0 
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Find proteins for A0A132NRN1 (Giardia intestinalis assemblage B)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL30Z [auth F]235Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL31AA [auth d]106Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL32BA [auth e]136Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL34CA [auth g]120Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL33DA [auth f]123Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL36EA [auth i]90Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL38FA [auth k]77Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL42GA [auth o]106Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL22HA [auth U]171Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL30IA [auth c]109Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL37JA [auth j]100Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL39KA [auth l]51Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL40LA [auth m]127Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL2MA [auth A]251Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL41NA [auth n]25Giardia intestinalis assemblage AMutation(s): 0 
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Entity ID: 41
MoleculeChains LengthOrganismImage
5S rRNAOA [auth 3]120Giardia intestinalis assemblage A
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Entity ID: 42
MoleculeChains LengthOrganismImage
5.8S rRNAPA [auth 4]141Giardia intestinalis assemblage A
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Entity ID: 43
MoleculeChains LengthOrganismImage
28S rRNAQA [auth 1]2,687Giardia intestinalis assemblage A
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

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GB [auth 1]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
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VA [auth j],
WA [auth m]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AC [auth 1]
AI [auth 1]
BC [auth 1]
CC [auth 1]
HB [auth 1]
AC [auth 1],
AI [auth 1],
BC [auth 1],
CC [auth 1],
HB [auth 1],
IB [auth 1],
JB [auth 1],
KB [auth 1],
LB [auth 1],
MB [auth 1],
NB [auth 1],
OB [auth 1],
PB [auth 1],
QB [auth 1],
RA [auth B],
RB [auth 1],
SB [auth 1],
TB [auth 1],
UB [auth 1],
VB [auth 1],
WB [auth 1],
XA [auth A],
XB [auth 1],
YB [auth 1],
YH [auth 1],
ZB [auth 1],
ZH [auth 1]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 4]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
AB [auth 4],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
BB [auth 4],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
CB [auth 4],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
DB [auth 4],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
SA [auth a],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
TA [auth V],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
UA [auth P],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
YA [auth 3],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
ZA [auth 4],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AH [auth 1]
BH [auth 1]
CH [auth 1]
DH [auth 1]
EB [auth 4]
AH [auth 1],
BH [auth 1],
CH [auth 1],
DH [auth 1],
EB [auth 4],
EH [auth 1],
FB [auth 4],
FH [auth 1],
GH [auth 1],
HH [auth 1],
IH [auth 1],
JH [auth 1],
KH [auth 1],
LH [auth 1],
MH [auth 1],
NH [auth 1],
OH [auth 1],
PH [auth 1],
QH [auth 1],
RH [auth 1],
SH [auth 1],
TG [auth 1],
TH [auth 1],
UG [auth 1],
UH [auth 1],
VG [auth 1],
VH [auth 1],
WG [auth 1],
WH [auth 1],
XG [auth 1],
XH [auth 1],
YG [auth 1],
ZG [auth 1]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118070
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R21AI149210
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128680

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