9FRK image
Deposition Date 2024-06-19
Release Date 2025-01-15
Last Version Date 2025-01-15
Entry Detail
PDB ID:
9FRK
Keywords:
TRANSLATION
Title:
Cryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to SD mRNA
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Saccharolobus solfataricus P2 (Taxon ID: 273057)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9FRK validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:rRNA 16S
Chain IDs:A (auth: 2)
Chain Length:1497
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8
Gene (Uniprot):rpl7ae
Chain IDs:BA (auth: 3)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P55858 Pfam ID:PF01248
Polymer Type:polyribonucleotide
Molecule:tRNA Met initiator
Chain IDs:GA (auth: 4)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA aEF1A
Chain IDs:HA (auth: 5)
Chain Length:28
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1
Gene (Uniprot):rps3ae
Chain IDs:B (auth: A)
Chain Length:72
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UXD4 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rps2
Chain IDs:C (auth: B)
Chain Length:231
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P95993 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
Gene (Uniprot):SSO5343
Chain IDs:D (auth: C)
Chain Length:65
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980V0 Pfam ID:PF07754
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rps4
Chain IDs:E (auth: D)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P95987 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4
Gene (Uniprot):rps4e
Chain IDs:F (auth: E)
Chain Length:52
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UX94 Pfam ID:PF08071, PF01479, PF00900
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rps5
Chain IDs:G (auth: F)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UX87 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS6
Gene (Uniprot):rps6e
Chain IDs:H (auth: G)
Chain Length:214
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980A6 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rps7
Chain IDs:I (auth: H)
Chain Length:193
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P35026 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rps8
Chain IDs:J (auth: I)
Chain Length:133
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UX92 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS8
Gene (Uniprot):rps8e
Chain IDs:K (auth: J)
Chain Length:133
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980W3 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rps9
Chain IDs:L (auth: K)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P95992 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rps10
Chain IDs:M (auth: L)
Chain Length:102
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P35027 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rps11
Chain IDs:N (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P95988 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rps12
Chain IDs:O (auth: N)
Chain Length:147
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P39573 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rps13
Chain IDs:P (auth: O)
Chain Length:165
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:P95986 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rps14
Chain IDs:Q (auth: P)
Chain Length:54
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZQ5 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rps15
Chain IDs:R (auth: Q)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980A8 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rps17
Chain IDs:S (auth: R)
Chain Length:114
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UX98 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17
Gene (Uniprot):rps17e
Chain IDs:T (auth: S)
Chain Length:79
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980K7 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rps19
Chain IDs:U (auth: T)
Chain Length:140
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UXA3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19
Gene (Uniprot):rps19E
Chain IDs:V (auth: U)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980F7 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS24
Gene (Uniprot):rps24e
Chain IDs:W (auth: V)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZY6 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS27
Gene (Uniprot):rps27e
Chain IDs:X (auth: W)
Chain Length:66
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97Z80 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS28
Gene (Uniprot):rps28e
Chain IDs:Y (auth: X)
Chain Length:83
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q980Q5 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS31
Gene (Uniprot):rps27ae
Chain IDs:Z (auth: Y)
Chain Length:75
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZY7 Pfam ID:PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rps3
Chain IDs:AA (auth: Z)
Chain Length:229
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q9UXA0 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:aS34
Gene (Uniprot):SSO6759
Chain IDs:CA (auth: a)
Chain Length:72
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZK4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS25
Gene (Uniprot):rps25e
Chain IDs:DA (auth: c)
Chain Length:65
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZZ6 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:VapB-type antitoxin
Gene (Uniprot):Ssol_1835
Chain IDs:EA (auth: d)
Chain Length:181
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:D0KTI0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein S30E (Rps30E)
Gene (Uniprot):rps30E
Chain IDs:FA (auth: e)
Chain Length:52
Number of Molecules:1
Biological Source:Saccharolobus solfataricus P2
UniProt ID:Q97ZH4 Pfam ID:PF04758
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU GA U modified residue
5MC A C modified residue
5MU GA U modified residue
6MZ A A modified residue
A2M A A modified residue
H2U GA U modified residue
MA6 A A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU GA U modified residue
Ligand Molecules
MG
SPM
ZN
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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Chemical

Disease

Primary Citation of related structures
9FRK