RCSB PDB - 9FRK: Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA

 9FRK

Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.

Bourgeois, G.Coureux, P.D.Lazennec-Schurdevin, C.Madru, C.Gaillard, T.Duchateau, M.Chamot-Rooke, J.Bourcier, S.Mechulam, Y.Schmitt, E.

(2025) Nat Commun 16: 348-348

  • DOI: https://doi.org/10.1038/s41467-024-55718-5
  • Primary Citation of Related Structures:  
    9FHL, 9FRA, 9FRK, 9FRL, 9FS6, 9FS8, 9FSF, 9FY0

  • PubMed Abstract: 

    The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus, a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5'-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3' end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation.


  • Organizational Affiliation

    Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, 91120, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1B [auth A]208Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q9UXD4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2C [auth B]231Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for P95993 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing proteinD [auth C]65Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q980V0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4E [auth D]181Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4F [auth E]239Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q9UX94 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5G [auth F]214Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6H [auth G]214Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7I [auth H]193Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for P35026 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8J [auth I]133Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q9UX92 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8K [auth J]133Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q980W3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9L [auth K]137Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for P95992 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10M [auth L]102Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for P35027 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11N [auth M]132Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12O [auth N]147Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for P39573 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13P [auth O]165Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14Q [auth P]54Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q97ZQ5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15R [auth Q]152Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q980A8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17S [auth R]114Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q9UX98 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17T [auth S]79Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q980K7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19U [auth T]140Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q9UXA3 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19V [auth U]158Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q980F7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24W [auth V]120Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q97ZY6 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27X [auth W]66Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
Find proteins for Q97Z80 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28Y [auth X]83Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS31Z [auth Y]75Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3AA [auth Z]229Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8BA [auth 3]127Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
aS34CA [auth a]72Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25DA [auth c]110Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
VapB-type antitoxinEA [auth d]72Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein S30E (Rps30E)FA [auth e]52Saccharolobus solfataricus P2Mutation(s): 0 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
AD [auth 2]
BD [auth 2]
CD [auth 2]
DD [auth 2]
ED [auth 2]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE [auth P]
BE [auth R]
DE [auth W]
EE [auth a]
FE [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
BB [auth 2]
BC [auth 2]
CB [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release