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- EMDB-50709: Cryo-EM structure of Saccharolobus solfataricus 30S initiation co... -

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Basic information

Entry
Database: EMDB / ID: EMD-50709
TitleCryo-EM structure of Saccharolobus solfataricus 30S initiation complex bound to Ss-MAP leaderless mRNA
Map data
Sample
  • Complex: High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA
    • RNA: x 3 types
    • Protein or peptide: x 25 types
  • RNA: x 1 types
  • Protein or peptide: x 6 types
  • Ligand: x 4 types
Keywords30S / ribosome / Translation / 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 / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding ...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 / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / 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 S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / 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 S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / 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 S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / 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 S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1.
Similarity search - Domain/homology
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 ...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 speciesSaccharolobus solfataricus P2 (archaea) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBourgeois G / Coureux PD / Mechulam Y / Schmitt E
Funding support France, 1 items
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, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50709.png

Downloads & links

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Map

FileDownload / File: emd_50709.map.gz / Format: CCP4 / Size: 320.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 438 pix.
= 365.292 Å		0.83 Å/pix.
x 438 pix.
= 365.292 Å		0.83 Å/pix.
x 438 pix.
= 365.292 Å

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Voxel sizeX=Y=Z: 0.834 Å
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Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.014759537 - 0.049936436
Average (Standard dev.)0.000069634334 (±0.0020652376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions438438438
Spacing438438438
CellA=B=C: 365.292 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50709_msk_1.map
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Additional map: #5

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Additional map: #4

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Additional map: #3

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Additional map: #2

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Additional map: #1

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Half map: #2

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Half map: #1

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Sample components

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Entire : High-resolution cryo-EM structure of Saccharolobus solfataricus 3...

EntireName: High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA
Components
  • Complex: High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA
    • RNA: rRNA 16S
    • Protein or peptide: Small ribosomal subunit protein eS1
    • Protein or peptide: Small ribosomal subunit protein uS2
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: Small ribosomal subunit protein eS4
    • Protein or peptide: Small ribosomal subunit protein eS6
    • Protein or peptide: Small ribosomal subunit protein uS7
    • Protein or peptide: Small ribosomal subunit protein uS8
    • Protein or peptide: Small ribosomal subunit protein eS8
    • Protein or peptide: Small ribosomal subunit protein uS9
    • Protein or peptide: Small ribosomal subunit protein uS10
    • Protein or peptide: Small ribosomal subunit protein uS11
    • Protein or peptide: Small ribosomal subunit protein uS12
    • Protein or peptide: Small ribosomal subunit protein uS13
    • Protein or peptide: Small ribosomal subunit protein uS15
    • Protein or peptide: Small ribosomal subunit protein eS17
    • Protein or peptide: Small ribosomal subunit protein uS19
    • Protein or peptide: Small ribosomal subunit protein eS19
    • Protein or peptide: Small ribosomal subunit protein eS24
    • Protein or peptide: Small ribosomal subunit protein eS28
    • Protein or peptide: Small ribosomal subunit protein eS31
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: Large ribosomal subunit protein eL8
    • Protein or peptide: Small ribosomal subunit protein eS25
    • Protein or peptide: VapB-type antitoxin
    • Protein or peptide: LSU ribosomal protein S30E (Rps30E)
    • RNA: mRNA_Map
    • RNA: tRNA initiator Met
  • RNA: mRNA_Map
  • Protein or peptide: Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
  • Protein or peptide: Small ribosomal subunit protein uS5
  • Protein or peptide: Small ribosomal subunit protein uS14
  • Protein or peptide: Small ribosomal subunit protein uS17
  • Protein or peptide: Small ribosomal subunit protein eS27
  • Protein or peptide: aS34
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMINE
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: High-resolution cryo-EM structure of Saccharolobus solfataricus 3...

SupramoleculeName: High-resolution cryo-EM structure of Saccharolobus solfataricus 30S ribosomal subunit bound to mRNA and initiator tRNA
type: complex / ID: 1 / Parent: 0
Macromolecule list: #1-#3, #5-#6, #8-#16, #18, #20-#23, #25-#28, #30-#34
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)

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Macromolecule #1: rRNA 16S

MacromoleculeName: rRNA 16S / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 486.375844 KDa
SequenceString: AAAUCCGGUU GAUCC(OMU)GCCG GACCCGACCG CUAUCGGGGU GGGGCUAAGC CA(OMU)GGGAGUC GUACGCUCCC GG GCAAGGG AGCGUGGCGG ACGGCUGAGU AACACGUGGC UAAC(OMC)UACCC UGAGGAGGGA GAUAACCCCG GGAAACUGG GGAUAAUCUC ...String:
AAAUCCGGUU GAUCC(OMU)GCCG GACCCGACCG CUAUCGGGGU GGGGCUAAGC CA(OMU)GGGAGUC GUACGCUCCC GG GCAAGGG AGCGUGGCGG ACGGCUGAGU AACACGUGGC UAAC(OMC)UACCC UGAGGAGGGA GAUAACCCCG GGAAACUGG GGAUAAUCUC CCAUAGGCGA GGAGUCCUGG AACGGUUCCU CGCUGAAAGG CUCAUGGGCU AUUCCCCGCU CAUGAGCGCC UCAGGAUGG GGCUGCGGC(OMC) CAUCAGGUAG UUGGGGGGGU AAGGGCCCCC CAAGCCUAUA ACGGGUAGGG GCCGUGA GA GCGGGAG(OMC)CC CCAGUUGGGC ACUGAGACAA G(OMG)GCCCAGGC CCUACGGGGC GCACCAGGCG CGAAACGUCC CCAAUGCGC GGAAGCGUGA GGGC(OMG)CCACC CCGAGUGCUC CCGUAAGGGA GCUUUUCCCC GCUCUACAAA GGCGGGG GA AUAAGCGGGG GGCAAGUCUG GUGUCAG(OMC)CG CCGCGGUAAU (A2M)CCAGCCCCG CGAGUGGU(OMC)G GGACUC UUA CUGGGCCUAA AGCGC(OMC)CGUA GCC(OMG)GCCCGA CAAGUCACUC CUUAAAGACC CCGGCUCAAC CGGGGGAAU GGGGGUGAUA CUGUCGGGCU AGGGGGCGGG AGAGGCCAGC GGUACUCCCG GAGUAGGGGC GAAAUCCUCA GAUCUCGGGA (OMG)GACCACCA GUGGCGAAAG CGGCUGGCUA GAACGCGCC(OMC) GACGGUGAGG GGCGAAAGCC GGGGCAGCAA AAG GGAUUA GAUACCCCUG UAGUCCCGGC UGUAAACAAU GCAGGCUAGG UGUCACAUGG GCUUAGAGCC CAUGUGGUGC CGCA GGGAA GCCGUUAAGC CUGCCGCCUG GGGAGUACGG UCGCAA(OMG)ACU GAAACUUAAA GGAAUUGGCG GGGGAGCACC A CAAGG(OMG)GU GGAACCUGCG GCUCAAUU(OMG)G AG(C4J)CAACGCC UGGAAUCUUA CUAGGGGAGA CCGCAGGAUG ACGGCCAGG CUAACGACCU UGCCUGACUC GCGGAGAGGA GGUGCAUGGC C(OMG)UCGCCAGC UCGUG(OMU)UGUG AAA UGUCCU GUUAAGUCAG GCAA(OMC)(OMG)AGCG AGACCCCCAC CACUAGUUGG UAUCCUGGUC UCCGGGCCGG GACCAC ACU AGUGGGACUG CCGGCGUAAG CCGGAGGAGG GAGGGGGCCA CGGCAGGUCA GCAUGCCCCG AAACCCCUGG GCCGCAC GC (OMG)GGUUACAAU GGCAGGGACA GCGGGAUUCC GACCCCGAAA GGGGAAGGUA AUCCCUUAAA CCCUGCCGCA GUUG GGAUC GAGGGCUGAA ACUCGCCCUC GUGAACGAGG AAUCCCUAGU AACCGCAGAU CAACAAUCUG CGGUGAAUAC G (OMU)CCCUGCU CCUUGCACAC ACCG(OMC)C(5MC)GUC GCUCCACCCG AGUAGGAGAG GGGUGAGGCC CCUUGCCUUU GGGUGGGGG GUCGAGCUUC UCUCCUGCAA GGGGGGAGAA GUCGUA(6MZ)CAA GGUAG(4AC)(4AC)GUA GGGG(MA6) A(4AC)(4AC)U GCGGCUGGAU CACCUCC

GENBANK: GENBANK: AE006641.1

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Macromolecule #33: mRNA_Map

MacromoleculeName: mRNA_Map / type: rna / ID: 33 / Number of copies: 1
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 5.039946 KDa
SequenceString:
(ATP)UGACUGAGG AUGAA

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Macromolecule #34: tRNA initiator Met

MacromoleculeName: tRNA initiator Met / type: rna / ID: 34 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.833904 KDa
SequenceString:
AGCGGGG(4SU)GG AGCAGCCUGG (H2U)AGCUCGUCG GG(OMC)UCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCGGCCCC CGCUACCA

GENBANK: GENBANK: CP026027.1

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Macromolecule #35: mRNA_Map

MacromoleculeName: mRNA_Map / type: rna / ID: 35 / Number of copies: 1
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 4.959966 KDa
SequenceString:
(A3P)UGACUGAGG AUGAA

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Macromolecule #2: Small ribosomal subunit protein eS1

MacromoleculeName: Small ribosomal subunit protein eS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 23.581205 KDa
SequenceString: MSAKGGAIKD KWKMKKWYSV ITPKAFGEVS LGSTPAYDIT QTIGRRVETT LYDLTGDFSQ VYVHLYFKII GNEGDRLITR FVGHELSRD YLRSLIRRKS SKINSIFDVT TKDGYVVRVK GLVLTTYKCH QSQKTAIRKI INETVSKKAS ELSFDDFTQE V VFGRLANE ...String:
MSAKGGAIKD KWKMKKWYSV ITPKAFGEVS LGSTPAYDIT QTIGRRVETT LYDLTGDFSQ VYVHLYFKII GNEGDRLITR FVGHELSRD YLRSLIRRKS SKINSIFDVT TKDGYVVRVK GLVLTTYKCH QSQKTAIRKI INETVSKKAS ELSFDDFTQE V VFGRLANE IFEAAKKIYP LRKAEIEKTK VLKVPENLGK QVESSSVSSG

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #3: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 26.04316 KDa
SequenceString: MKVTNLSEKE ERGGELTEAE KEELRKSEKG AIIELLVPVD TYLSAGVHIG THSCTKYMES FVYRVRAEGL YVLDVRKIDE RLRIAAKFL SRYDPQDIIV VASRPYAYRP VQKFAEVVGS RALVGRIIPG TFTNPYLSTY IEPKVLLVSD PRTDTQAIKE A AKVGIPIV ...String:
MKVTNLSEKE ERGGELTEAE KEELRKSEKG AIIELLVPVD TYLSAGVHIG THSCTKYMES FVYRVRAEGL YVLDVRKIDE RLRIAAKFL SRYDPQDIIV VASRPYAYRP VQKFAEVVGS RALVGRIIPG TFTNPYLSTY IEPKVLLVSD PRTDTQAIKE A AKVGIPIV AFADTDAKID YIDLIIPANN KGRKSLALLY WALARQILRE RRVIPPDGDL AVPVSEFEMR LVQ

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #4: Small zinc finger protein HVO-2753-like zinc-binding pocket domai...

MacromoleculeName: Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 7.352656 KDa
SequenceString:
MSVKLSIREE VEPPICSSCG KIIHPREKGV EFYCPNCGEV LIRRDHMCRK QGAEYICPNC GFKGP

UniProtKB: Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein

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Macromolecule #5: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 20.7841 KDa
SequenceString:
MGDPKKSRKK WETPGHPWIK ERIGYEQELL GKYGLRNKRE IWIAQSIIRK FRHQARSLLA LPPAERAVRE KQLVGKLLKM GLLKKETAT VDDILSLTEQ DLLERRLQTI VYKKGLSNTI YQARQLITHG HIAVNGKRVT SPGYIVNVDE ENLIDYYVTS S FKSRPPVM SQQEGGEIGV KQA

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #6: Small ribosomal subunit protein eS4

MacromoleculeName: Small ribosomal subunit protein eS4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 27.564197 KDa
SequenceString: MAHITRFEAP WFLMISKKQY KWTVRPNAGP HSIEKSIPLA VVIRDYLKLA GTIREAKHII FDGKVLVDGK VRKDYKYPVG LMDIVSIPS ADLYFRVLPD NVRFMRFSKI SADEARYKYV RIINKTTIKE GRIQLNLEDG RNILVDKETA KNFKTLMTLK I ELPSQQIL ...String:
MAHITRFEAP WFLMISKKQY KWTVRPNAGP HSIEKSIPLA VVIRDYLKLA GTIREAKHII FDGKVLVDGK VRKDYKYPVG LMDIVSIPS ADLYFRVLPD NVRFMRFSKI SADEARYKYV RIINKTTIKE GRIQLNLEDG RNILVDKETA KNFKTLMTLK I ELPSQQIL DSFTISERSY AIFVGGRNVG IHGIVKNINL SKFKSRKYSV ITLESRDGNT YQTNIMNVMS IGREKSDLRV D

UniProtKB: Small ribosomal subunit protein eS4

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Macromolecule #7: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 23.275062 KDa
SequenceString: MAEEVPSLNI EEWKPRTSIG SLVKEGKISS IKELFDRNLP ITEPEIVDVL LPKLKYEVVD IKVVQKQTDA GEISRYKVLV IMGNMDGYV SIGTGKAKQL RVAIQKAIRD AKMNIIPVRR GCGSWQCTCG EPHSLPFKVV GKAGSVEVDL LPAPKGTGLV V GSVLKTLL ...String:
MAEEVPSLNI EEWKPRTSIG SLVKEGKISS IKELFDRNLP ITEPEIVDVL LPKLKYEVVD IKVVQKQTDA GEISRYKVLV IMGNMDGYV SIGTGKAKQL RVAIQKAIRD AKMNIIPVRR GCGSWQCTCG EPHSLPFKVV GKAGSVEVDL LPAPKGTGLV V GSVLKTLL TYAGIKDAWS TTKGETRTTE NFVRAGYSAL YNTYKFVTLQ DWV

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: Small ribosomal subunit protein eS6

MacromoleculeName: Small ribosomal subunit protein eS6 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 23.757402 KDa
SequenceString: MPDFKIVISD PQSVEPKRIK VKVKASDQVK SITGEKDGKA VPQAKVNEKT KQLLNVDTLL TLEITKQEGD KKVKVKGHFK VDVDNSVPD NEVWISKTMA EKFGAEDFEA FAYRTKTLQI SVDQNKATNL VGLKIGDVFE ANQLIGLPVK LKITGGSDNS G FPMRFDVI ...String:
MPDFKIVISD PQSVEPKRIK VKVKASDQVK SITGEKDGKA VPQAKVNEKT KQLLNVDTLL TLEITKQEGD KKVKVKGHFK VDVDNSVPD NEVWISKTMA EKFGAEDFEA FAYRTKTLQI SVDQNKATNL VGLKIGDVFE ANQLIGLPVK LKITGGSDNS G FPMRFDVI GAAKRKILLS GPPGFYPNEN GERRRKTIRG NTISQEIVQI NTIIVR

UniProtKB: Small ribosomal subunit protein eS6

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Macromolecule #9: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 22.035703 KDa
SequenceString: MSLENLQLDI KVFGKWDTKV EIRDPSLKKY ISLMPVYLPH TGGRHEHRRF GKAKVPIVER LINQIMRPGR NKGKKHLAYN IVKLAFDII YLKTGQNPIQ VLVRAIENSA PREEVTRIMY GGIVYYVAVD VSPQRRIDLA LRHIATGAKD ASFNNPKPIE E VLAEEIIA ...String:
MSLENLQLDI KVFGKWDTKV EIRDPSLKKY ISLMPVYLPH TGGRHEHRRF GKAKVPIVER LINQIMRPGR NKGKKHLAYN IVKLAFDII YLKTGQNPIQ VLVRAIENSA PREEVTRIMY GGIVYYVAVD VSPQRRIDLA LRHIATGAKD ASFNNPKPIE E VLAEEIIA AANNDSKSFA IKRKEEIERI ALSSR

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #10: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 15.083798 KDa
SequenceString:
MVFVNPLANA LTSIYNNEMR RNKQAIIMPA SKLVINVLRV MQKEGYVGEF EYIDDGRWGK ITVQLLGRVN KCGPITPRYP LSYRQMIAL PDYVRRYLPS KEIGIIIVST SKGVMSHKEA ARLRIGGVAL GYVY

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #11: Small ribosomal subunit protein eS8

MacromoleculeName: Small ribosomal subunit protein eS8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 14.685966 KDa
SequenceString:
MGFYQGPDNR KITGGLKGKH RDKRKYEIGN PPTFTTLSAE DIRIKDRTLG GNFKVRLKYT TTANVLDPAT NTAKKVKILE ILETPANKE LARRGIIIRG AKIRTEAGLA VVTSRPGQDG VINAVLLKNE SQRS

UniProtKB: Small ribosomal subunit protein eS8

+
Macromolecule #12: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 15.732472 KDa
SequenceString:
MSEEQKLVIS SARRKTARAT CYIYAGKGRV FVNNVPIELI PIEMVRLKIM EPLLLAGNDI RSKIDAKIIT YGGGIMGQAD AARMALARA LVKFTGSKEL EKIYRAYDRT MLAGDPRQTE SEKWMRYSAR RWRQKSYR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #13: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 12.13344 KDa
SequenceString:
MPTKARIRLW STNVENLNYV ITQIRGIVEK TGIEMRGPIP LPTSKLEVPI MRLPHGEGRK KWEKWEMRVH KRLIDIAADE RVMRQLMRV RVPEDVYIEI QLI

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #14: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 14.065243 KDa
SequenceString:
MSSRREIRWG IAHIYASQNN TLLTISDLTG AEIISRASGG MVVKADREKS SPYAAMLAAN KAASDALEKG IMALHIKVRA PGGYGSKTP GPGAQPAIRA LARAGFIIGR IEDVTPIPHD TIRRPGGRRG RRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #15: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 16.381561 KDa
SequenceString:
MVKSKSPKGI YAARKLRLKR LKFRRSQRKY KTKILKLKEK YDPLGGAPMA RGIVLEKVGI ESRQPNSAVR KCVRVQLVRN GRVVTAFVP GDGGVNFIDE HDEVIITGIG GTLGRSMGDL PGVRYKVIMV NGVSLDALYK GKKQKPVR

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #16: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 18.662439 KDa
SequenceString:
MSQQFKYVVR IFGQDVDGTM KLPYALAMVK GIGYNTAKAI IRKLGMDPNA RLGELSDAEV KKVESVISDH TIKGLPSWLY NRRKDYESG LDLHLVTSDL IFYVRNDIER EKKSRSWRGV RHSLGLKVRG QRTRTTGRTG MTIGVARKKA AQPQSQQSSS Q QQKSS

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #17: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 6.416507 KDa
SequenceString:
MGKYKPPAER KYGKGVQSCQ RCGSKDSVIQ KYGIYLCRQC FREVAYELGF RKYW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #18: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 17.475533 KDa
SequenceString:
MNKRRAKGKS HSIRPARAGA PKWVRLTREE VEMLVEELAK RGYTPSMIGI ILRDQYGIPL VKQIVGKKVT QILEERGLAP QIPEDLFNL IRKAVNVRRH INEYPRDKTA KKGLEEIESK IRRLTRYYKG IGKLPQEWVY DPAKAELLVA GAS

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #19: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 12.987173 KDa
SequenceString:
MVSKGKTVKD PGIPNITIPE KVCEDEDCPY HGSLRVRGIT LEGVIVKYRG TKAAVIERQY LYYDSKYKRY ERRRSRIHAH VPPCINVRE GDKVIIGECR PLSKSISFVV LGKVS

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #20: Small ribosomal subunit protein eS17

MacromoleculeName: Small ribosomal subunit protein eS17 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 9.64707 KDa
SequenceString:
MGNIYTKDIK RIVKEIYDRY KDEIKDDYNT NKQIVIRYVD VKSKKVRNRI AGYLTRYYKI MKEKETSPAE EKEEISEEI

UniProtKB: Small ribosomal subunit protein eS17

+
Macromolecule #21: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 16.399316 KDa
SequenceString:
MSLEIPPEWK NFKYRGKSID ELLNMPMDEF IKLLPSRQRR SLKRGFTDAQ RHLLEKVRKY RREGKFNKTI KTHVRNLVIL PELIGLKMA VYNGKEFVEF TVTPEMIGHY LGEYSITTKK VEHGEPGLKA TRSSLFLAMK G

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #22: Small ribosomal subunit protein eS19

MacromoleculeName: Small ribosomal subunit protein eS19 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 18.149432 KDa
SequenceString:
MSLIMITAEM VPPDLLIKRL AIYLKENVKT VDPPEWALLA KTASFKERVP DNAEDWWYIR AASLLRKLYV NSIIGIEKTR TIYGGRKRR GTRPEKFVKA PGHVNRLIFQ QLEKAGLVQK IKNKGRSLSP KGRSLLDKLA LEIFKELAEN NTSLKVYLE

UniProtKB: Small ribosomal subunit protein eS19

+
Macromolecule #23: Small ribosomal subunit protein eS24

MacromoleculeName: Small ribosomal subunit protein eS24 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 13.122204 KDa
SequenceString:
MESQAKVKIS DKAEGIIERD MQNSVIGRRE ISLKVYHMGS GTPSRKDIIK AIIQALGSQE NLVVVRKIST SYGAGISNVK LHIYKSREI LEKVEPKYLL DRDAGTKQKK GGSKGGQGAK G

UniProtKB: Small ribosomal subunit protein eS24

+
Macromolecule #24: Small ribosomal subunit protein eS27

MacromoleculeName: Small ribosomal subunit protein eS27 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 7.396945 KDa
SequenceString:
MMRKLRVLIP EPKSRFLRVK CPNCGNEQTI FSHATFPVRC LSCGTELVYS MGGKAKIVGE VVRIMG

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #25: Small ribosomal subunit protein eS28

MacromoleculeName: Small ribosomal subunit protein eS28 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 9.393792 KDa
SequenceString:
MSEKTQQSQG SSIIEEFGFP AEVIQILDRT GVTGEVTQVR VRVLEGRDKG RILTRNVKGP VRVGDILILR ETEREARKIT TKR

UniProtKB: Small ribosomal subunit protein eS28

+
Macromolecule #26: Small ribosomal subunit protein eS31

MacromoleculeName: Small ribosomal subunit protein eS31 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 8.703415 KDa
SequenceString:
MLELNKRKEE AKVAKEQKVK AIVRTYYVIE GNKVKLKNKK CPRCGSIMAH HLKPNERWSC GKCGYTEFIG ASKKR

UniProtKB: Small ribosomal subunit protein eS31

+
Macromolecule #27: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 25.862209 KDa
SequenceString: MPNIKRYFLE KSIVKVKIDE YLAKQYYNAE YAGVEVLKTP IGTRVIIYAG RPSMIIGRGG RNIKQLAQIF EKVFGLENPQ ITITNVENP ELNARVMAFR LAIALEKGYH FRRAAFISMR RIMNAGALGA EIIISGKLTT ERARYEKLKE GIVYKSGQQL E KMIDRAIA ...String:
MPNIKRYFLE KSIVKVKIDE YLAKQYYNAE YAGVEVLKTP IGTRVIIYAG RPSMIIGRGG RNIKQLAQIF EKVFGLENPQ ITITNVENP ELNARVMAFR LAIALEKGYH FRRAAFISMR RIMNAGALGA EIIISGKLTT ERARYEKLKE GIVYKSGQQL E KMIDRAIA IAMLKPGIFG VEVVITKPLK IEDKINLKES PSVPQEVSVT NVTFIEESSQ KSEEKSEGEK E

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #28: Large ribosomal subunit protein eL8

MacromoleculeName: Large ribosomal subunit protein eL8 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 13.757939 KDa
SequenceString:
MSKASYVKFE VPQDLADKVL EAVRKAKESG KIKKGTNETT KAVERGQAKL VIIAEDVQPE EIVAHLPLLC DEKKIPYVYV SSKKALGEA CGLQVATASA AILEPGEAKD LVDEIIKRVN EIKGKTSS

UniProtKB: Large ribosomal subunit protein eL8

+
Macromolecule #29: aS34

MacromoleculeName: aS34 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 8.2108 KDa
SequenceString:
MSIKNRGSNA YGHLGWLTVY CRICNRKLII GTDILYKCPK CEKKYSAYFC EADKRGLKGK CPYCGTELVP IL

UniProtKB: Uncharacterized protein

+
Macromolecule #30: Small ribosomal subunit protein eS25

MacromoleculeName: Small ribosomal subunit protein eS25 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 12.372557 KDa
SequenceString:
MGGASKKPIS TMEKRLKKEA EKQQKAEEKK KGPSKTGKEI ISRAVTIDEE TKKKVLDEIK KESIITPYAL ATKSGISISV ARKILKELE NQNVVKLYSK NRRLEIYIAA S

UniProtKB: Small ribosomal subunit protein eS25

+
Macromolecule #31: VapB-type antitoxin

MacromoleculeName: VapB-type antitoxin / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 8.392802 KDa
SequenceString:
MEMLKIKLSS GREVEINDDT IAVLNEYVRT QMTLEELSKR LGLSGWEEAY ELIKQVPAWV MWSPLPIYKK LA

UniProtKB: Uncharacterized protein

+
Macromolecule #32: LSU ribosomal protein S30E (Rps30E)

MacromoleculeName: LSU ribosomal protein S30E (Rps30E) / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Molecular weightTheoretical: 6.064125 KDa
SequenceString:
MPSHGSLTKA GKVRSQTPKI QPKEKHKEVP RVRNRKEYEK RVVKARQQAP AR

UniProtKB: LSU ribosomal protein S30E (Rps30E)

+
Macromolecule #36: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 58 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #37: SPERMINE

MacromoleculeName: SPERMINE / type: ligand / ID: 37 / Number of copies: 42 / Formula: SPM
Molecular weightTheoretical: 202.34 Da
Chemical component information

ChemComp-SPM:
SPERMINE

+
Macromolecule #38: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 38 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #39: water

MacromoleculeName: water / type: ligand / ID: 39 / Number of copies: 221 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9fhl

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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