9FRL image
Entry Detail
PDB ID:
9FRL
EMDB ID:
Keywords:
Title:
Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA with h44 in up position
Biological Source:
PDB Version:
Deposition Date:
2024-06-19
Release Date:
2025-01-15
Method Details:
Experimental Method:
Resolution:
2.97 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:rRNA 16S
Chain IDs:A (auth: 2)
Chain Length:1497
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein eL8
Chain IDs:X (auth: 3)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polyribonucleotide
Description:tRNA Met initiator
Chain IDs:AA (auth: 4)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:BA (auth: 5)
Chain Length:28
Number of Molecules:1
Biological Source:Pyrococcus abyssi
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS1
Chain IDs:B (auth: A)
Chain Length:208
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:C (auth: B)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
Chain IDs:D (auth: C)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS4
Chain IDs:E (auth: D)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS4
Chain IDs:HA (auth: E)
Chain Length:52
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS5
Chain IDs:F
Chain Length:214
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS6
Chain IDs:G
Chain Length:214
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS7
Chain IDs:H
Chain Length:193
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS8
Chain IDs:I
Chain Length:133
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS8
Chain IDs:J
Chain Length:133
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS9
Chain IDs:K
Chain Length:137
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS10
Chain IDs:L
Chain Length:102
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS11
Chain IDs:M
Chain Length:132
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:N
Chain Length:147
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS13
Chain IDs:O
Chain Length:165
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS14
Chain IDs:CA (auth: P)
Chain Length:54
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:P (auth: Q)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS17
Chain IDs:DA (auth: R)
Chain Length:114
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS17
Chain IDs:Q (auth: S)
Chain Length:79
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:R (auth: T)
Chain Length:140
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS19
Chain IDs:S (auth: U)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS24
Chain IDs:T (auth: V)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS27
Chain IDs:U (auth: W)
Chain Length:66
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS28
Chain IDs:V (auth: X)
Chain Length:83
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS31
Chain IDs:W (auth: Y)
Chain Length:75
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS3
Chain IDs:EA (auth: Z)
Chain Length:229
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:aS34
Chain IDs:Y (auth: a)
Chain Length:208
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein eS25
Chain IDs:GA (auth: c)
Chain Length:110
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:aS33
Chain IDs:FA (auth: d)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Polymer Type:polypeptide(L)
Description:LSU ribosomal protein S30E (Rps30E)
Chain IDs:Z (auth: e)
Chain Length:52
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU AA U modified residue
5MC A C modified residue
5MU AA U modified residue
6MZ A A modified residue
A2M A A modified residue
H2U AA U modified residue
MA6 A A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU AA U modified residue
Primary Citation
Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.
Nat Commun 16 348 348 (2025)
PMID: 39753558 DOI: 10.1038/s41467-024-55718-5

Abstact

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.

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Primary Citation of related structures