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- PDB-9fra: Cryo-EM structure of Saccharolobus solfataricus 30S initiation co... -

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Entry
Database: PDB / ID: 9fra
TitleCryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA
Components
  • (Small ribosomal subunit protein ...) x 26
  • (mRNA_Map) x 2
  • LSU ribosomal protein S30E (Rps30E)
  • Large ribosomal subunit protein eL8
  • Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
  • VapB-type antitoxin
  • aS34
  • rRNA 16S
  • tRNA initiator Met
KeywordsTRANSLATION / 30S / ribosome / Saccharolobus solfataricus
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S30 / Ribosomal protein S17e signature. / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S27e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / : / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain
Similarity search - Domain/homology
SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 ...SPERMINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / LSU ribosomal protein S30E (Rps30E) / Uncharacterized protein / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS28 / Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharolobus solfataricus P2 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBourgeois, G. / Coureux, P.D. / Mechulam, Y. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2025
Title: Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity.
Authors: Gabrielle Bourgeois / Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Clément Madru / Thomas Gaillard / Magalie Duchateau / Julia Chamot-Rooke / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
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, ...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.
History
DepositionJun 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: rRNA 16S
A: Small ribosomal subunit protein eS1
B: Small ribosomal subunit protein uS2
C: Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein eS4
F: Small ribosomal subunit protein uS5
G: Small ribosomal subunit protein eS6
H: Small ribosomal subunit protein uS7
I: Small ribosomal subunit protein uS8
J: Small ribosomal subunit protein eS8
K: Small ribosomal subunit protein uS9
L: Small ribosomal subunit protein uS10
M: Small ribosomal subunit protein uS11
N: Small ribosomal subunit protein uS12
O: Small ribosomal subunit protein uS13
P: Small ribosomal subunit protein uS14
Q: Small ribosomal subunit protein uS15
R: Small ribosomal subunit protein uS17
S: Small ribosomal subunit protein eS17
T: Small ribosomal subunit protein uS19
U: Small ribosomal subunit protein eS19
V: Small ribosomal subunit protein eS24
W: Small ribosomal subunit protein eS27
X: Small ribosomal subunit protein eS28
Y: Small ribosomal subunit protein eS31
Z: Small ribosomal subunit protein uS3
3: Large ribosomal subunit protein eL8
a: aS34
c: Small ribosomal subunit protein eS25
d: VapB-type antitoxin
e: LSU ribosomal protein S30E (Rps30E)
5: mRNA_Map
4: tRNA initiator Met
s: mRNA_Map
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,007,131143
Polymers996,70035
Non-polymers10,431108
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules 254s

#1: RNA chain rRNA 16S


Mass: 486375.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: GenBank: AE006641.1
#33: RNA chain mRNA_Map


Mass: 5039.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)
#34: RNA chain tRNA initiator Met


Mass: 24833.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1334604293
#35: RNA chain mRNA_Map


Mass: 4959.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)

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Small ribosomal subunit protein ... , 26 types, 26 molecules ABDEFGHIJKLMNOPQRSTUVWXYZc

#2: Protein Small ribosomal subunit protein eS1 / 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 23581.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UXD4
#3: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26043.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P95993
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 20784.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P95987
#6: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 27564.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UX94
#7: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 23275.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UX87
#8: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 23757.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980A6
#9: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 22035.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P35026
#10: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 15083.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UX92
#11: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 14685.966 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980W3
#12: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 15732.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P95992
#13: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 12133.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P35027
#14: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14065.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P95988
#15: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 16381.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P39573
#16: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 18662.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P95986
#17: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 6416.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZQ5
#18: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 17475.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980A8
#19: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 12987.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UX98
#20: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 9647.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980K7
#21: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 16399.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UXA3
#22: Protein Small ribosomal subunit protein eS19


Mass: 18149.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980F7
#23: Protein Small ribosomal subunit protein eS24 / 30S ribosomal protein S24e


Mass: 13122.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZY6
#24: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 7396.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97Z80
#25: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 9393.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980Q5
#26: Protein Small ribosomal subunit protein eS31 / 30S ribosomal protein S27ae


Mass: 8703.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZY7
#27: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 25862.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q9UXA0
#30: Protein Small ribosomal subunit protein eS25 / 30S ribosomal protein S25e


Mass: 12372.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZZ6

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Protein , 5 types, 5 molecules C3ade

#4: Protein Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein


Mass: 7352.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q980V0
#28: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13757.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: P55858
#29: Protein aS34


Mass: 8210.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZK4
#31: Protein VapB-type antitoxin / aS33


Mass: 8392.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: D0KTI0
#32: Protein LSU ribosomal protein S30E (Rps30E)


Mass: 6064.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus P2 (archaea) / References: UniProt: Q97ZH4

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Non-polymers , 4 types, 329 molecules

#36: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: Mg
#37: Chemical...
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C10H26N4
#38: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#39: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA
Type: RIBOSOME
Entity ID: #1-#3, #5-#6, #8-#16, #18, #20-#23, #25-#28, #30-#34
Source: RECOMBINANT
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00470956
ELECTRON MICROSCOPYf_angle_d0.625103451
ELECTRON MICROSCOPYf_dihedral_angle_d15.80832143
ELECTRON MICROSCOPYf_chiral_restr0.03812770
ELECTRON MICROSCOPYf_plane_restr0.0057044

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