6SWD

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.

Coureux, P.D.Lazennec-Schurdevin, C.Bourcier, S.Mechulam, Y.Schmitt, E.

(2020) Commun Biol 3: 58-58

  • DOI: https://doi.org/10.1038/s42003-020-0780-0
  • Primary Citation of Related Structures:  
    6SW9, 6SWC, 6SWD, 6SWE

  • PubMed Abstract: 

    Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA i Met . Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA i Met complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N 4 -acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.


  • Organizational Affiliation

    Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128, Palaiseau, cedex, France. pierre-damien.coureux@polytechnique.edu.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3AeB [auth A]199Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
Find proteins for Q9V2K7 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2C [auth B]202Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Zn-ribbon RNA-binding protein involved in translationD [auth C]63Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4E [auth D]180Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4eF [auth E]243Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5G [auth F]236Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6eH [auth G]125Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8e127Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth M]137Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth N]147Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15M [auth Q]158Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17N [auth R]113Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S24eO [auth V]99Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S27eP [auth W]65Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein aL41Q [auth 0]36Pyrococcus abyssi GE5Mutation(s): 0 
UniProt
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor 1AS [auth 6]113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eIF1Aaif1APYRAB05910PAB2441
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth 2]1,044Pyrococcus abyssi GE5
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Entity ID: 18
MoleculeChains LengthOrganismImage
mRNAR [auth 5]20Pyrococcus abyssi GE5
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
RA [auth C],
SA [auth C],
TA [auth F],
UA [auth R],
VA [auth W]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 2]
BA [auth 2]
CA [auth 2]
DA [auth 2]
EA [auth 2]
AA [auth 2],
BA [auth 2],
CA [auth 2],
DA [auth 2],
EA [auth 2],
FA [auth 2],
GA [auth 2],
HA [auth 2],
IA [auth 2],
JA [auth 2],
KA [auth 2],
LA [auth 2],
MA [auth 2],
NA [auth 2],
OA [auth 2],
PA [auth 2],
QA [auth 2],
T [auth 2],
U [auth 2],
V [auth 2],
W [auth 2],
WA [auth 5],
X [auth 2],
Y [auth 2],
Z [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE11-0037

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection, Database references