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- EMDB-14731: High-resolution cryo-EM structure of Pyrococcus abyssi 30S riboso... -

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Basic information

Entry
Database: EMDB / ID: EMD-14731
TitleHigh-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop
Map data
Sample
  • Complex: High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA
    • Complex: High resolution 30S ribosomal subunit with a fragment of mRNA
      • RNA: x 2 types
      • Protein or peptide: x 28 types
    • Complex: Met-tRNAiMet
      • RNA: x 1 types
  • Ligand: x 3 types
KeywordsInitiation complex / translation initiation / small ribosomal subunit / aIF5b / TRANSLATION
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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 S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 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 S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S3Ae / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / 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 / Ribosomal protein S2 signature 2. / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile.
Similarity search - Domain/homology
Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS27 ...Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsKazan R / Bourgeois G / Mechulam Y / Coureux PD / Schmitt E
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Role of aIF5B in archaeal translation initiation.
Authors: Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt /
Abstract: In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
History
DepositionApr 6, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14731.png

Downloads & links

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Map

FileDownload / File: emd_14731.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 432 pix.
= 371.52 Å		0.86 Å/pix.
x 432 pix.
= 371.52 Å		0.86 Å/pix.
x 432 pix.
= 371.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0249
Minimum - Maximum-0.14437886 - 0.3357949
Average (Standard dev.)0.0002494454 (±0.009355333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 371.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_14731_additional_1.map
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Half map: #2

Fileemd_14731_half_map_1.map
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Half map: #1

Fileemd_14731_half_map_2.map
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Sample components

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Entire : High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA

EntireName: High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA
Components
  • Complex: High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA
    • Complex: High resolution 30S ribosomal subunit with a fragment of mRNA
      • RNA: rRNA 16S
      • Protein or peptide: 30S ribosomal protein S3Ae
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: Zn-ribbon RNA-binding protein involved in translation
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S4e
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6e
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S8e
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14 type Z
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S17e
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S19e
      • Protein or peptide: 30S ribosomal protein S24e
      • Protein or peptide: 30S ribosomal protein S27e
      • Protein or peptide: 30S ribosomal protein S28e
      • Protein or peptide: 30S ribosomal protein S27ae
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 50S ribosomal protein L41e
      • Protein or peptide: 50S ribosomal protein L7Ae
      • RNA: mRNA
    • Complex: Met-tRNAiMet
      • RNA: Met-tRNAiMet
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA

SupramoleculeName: High resolution 30S ribosomal subunit with a fragment of mRNA and tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31

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Supramolecule #2: High resolution 30S ribosomal subunit with a fragment of mRNA

SupramoleculeName: High resolution 30S ribosomal subunit with a fragment of mRNA
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#30
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Supramolecule #3: Met-tRNAiMet

SupramoleculeName: Met-tRNAiMet / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #31
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Macromolecule #1: rRNA 16S

MacromoleculeName: rRNA 16S / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 487.993062 KDa
SequenceString: AUUC(4AC)GG(OMU)UG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC A(OMU)GCGAGUCA AGGG GGCGU CCCUUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAAC(OMC)UA CCCUCGGGAG GGGGAUAACC C CGGGAAAC ...String:
AUUC(4AC)GG(OMU)UG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC A(OMU)GCGAGUCA AGGG GGCGU CCCUUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAAC(OMC)UA CCCUCGGGAG GGGGAUAACC C CGGGAAAC UGGGGCUAAU CCCCCAUAGG CCUGGGGUAC UGGAAGGUCC CCAGGCCGAA AGGGAGCCGU AAGGCUCCGC CC GAGGAUG GGCCGGCGGC (LHH)GAUUAGGUA GUUGGUGGGG UAACGGCCCA CCAAGC(4AC)GAA GAUCGGUACG GGC (4AC)GUGAG AGCGGGAGCC (4AC)GGAGAUGGA CACUGAGACA CGGGUCCAGG CCCUACGGGG CGCAGCAGGC GCGA (A2M)ACCU C(4AC)GCAAUGCG GGAAAC(4AC)GCG ACGGGGGGAC CCCCAGUGCC GUGCCUCUGG CACGGCUUUU CCG GAGUGU AAAAAGCUCC GGGAAUAAGG (OMG)CUG(OMG)GCAAG GC(4AC)GGUGGCA GCCGCCGCGG UAAUACCGGC GG CC(4AC)GAGU GGU(OMG)GCCACU AUUAUUGGG(5MC) CUAAAGCGGC (4AC)GUAGCCGGG CCCGUAAGUC CCUGGCG AA AUCCCACGGC UCAAC(4AC)GUGG GGCUCGCUGG GGAUACUGCG GGCCUUGGGA C(4AC)GGGAGAGG C(4AC)GGGG GUA CCCCCGGGGU AGG(OMG)GUGAAA UCCUAUAAUC CCGGGG(OMG)GAC CGCCAGUGG(5MC) GAAGGCGCC(4AC) G GCUGGAAC GGGUC(4AC)GACG GUGAGGGC(4AC)G AAGGCCAGGG GAGCGAAC(4AC)G GAUUAGAUAC CCGGGUAGUC (OMC)(OMU)GGCUGUA AAGGA(OMU)GCGG GCUAGGUGUC GGGCGAGCUU CGAGCUCGCC CGGUGC(4AC)G(OMU)A G GGAAGC(4AC)G UUAAG(OMC)C(4AC)GC (4AC)GCCUGGGGA GUACGGC(4AC)GC AA(OMG)G(5MC)UGAAA CUUA AAGGA AUUGGCGGGG GAGCACUACA AGG(OMG)GUGGAG CGUGCGGUUU AAUU(OMG)GAU(B8H)C AACGCCGGGA ACC UCAC(4AC)G GGGGCGACGG CAGGAUGAAG GCCAGGCUGA AGGUCUUGCC GGACGCGCCG AGAGGAGGUG CAUGGC (5MC)GC (4AC)GUCAGCU(OMC)G UA(OMC)(LHH)GUGAGG CGUCCACUUA AGUGUGGUAA C(OMG)AGCGAGAC CCG CGCCCC CAGUUGCCAG UCCCUCCCGC UCGGGAGGGA GGCACUCUGG GGGGACUGCC GGCGAUAAGC (4AC)GGAGGAAGG GGCGGGCGA CGGUAGGUCA G(OMU)AUGCCC(4AC)G AAACCCCCGG GCUACA(5MC)GCG CGCUACAAUG GGCGGGACA AUGGGUGC(4AC)G ACCC(4AC)GAAAG GGGGAGGUAA UCCCCUAAAC CCGCCCUCAG UUCGGAUCGC GGGCUGCAAC UC GCCCGCG UGAAGCUGGA AUCCCUAGUA CCCGCGCGUC AUCAUCGCGC GGCGAAUACG UCCCUGCUCC UUGCACACAC (5MC)G(OMC)CCG(OMU)CA CUCCACCCGA GCGGGGCCUA GGUGAGGCCC GAUCUCCUUC GGGAGGUCGG GUCGAGCCU AGGCUCCGUG AGGGGGGAGA AGUCG(UR3)A(6MZ)CA AGGUAGC(4AC)GU AGGGG(MA6)(MA6)CCU ACGG(5MC)U (5MC)GA UCAC(5MC)UCCU

GENBANK: GENBANK: AJ248283.1

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Macromolecule #30: mRNA

MacromoleculeName: mRNA / type: rna / ID: 30 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 5.509302 KDa
SequenceString:
UGGAGGUGAU UUAAAUG

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Macromolecule #31: Met-tRNAiMet

MacromoleculeName: Met-tRNAiMet / type: rna / ID: 31 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
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 #2: 30S ribosomal protein S3Ae

MacromoleculeName: 30S ribosomal protein S3Ae / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 22.888068 KDa
SequenceString: MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA ...String:
MAAKRRVSAA KDKWKLKQWY VIYAPDFFGG VEVGLTPADD PEKVLNRVVE VTLKDITGDF LKGHVKLYFQ VYDVKGQNAY TKFKGMKLA RSYIRSLVRR RTTRIDGIFN ITTKDGYKLR VMAMVIAARR IQTSQERAIR KIMQEIIYKK AEELNFKDFV L EAVNGKIA AEIAKEAKKI YPLKKAEIRK IKVLGEPEVA A

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #3: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 23.026865 KDa
SequenceString: MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY ...String:
MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA RFDPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVIIITD PRADHQAMKE AIEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY WILAREILYN RGEISSREEF KIPVEEFEMK IVRR

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation

MacromoleculeName: Zn-ribbon RNA-binding protein involved in translation / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 7.163395 KDa
SequenceString:
MAENVELKFE IPVCTSCGRE ITPREHATHF VCPNCGEAII WRCETCRLLA KPYKCPKCGW EGP

UniProtKB: Zn-ribbon RNA-binding protein involved in translation

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Macromolecule #5: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 21.38191 KDa
SequenceString:
MGDPKRQRKK YETPPHPWIK ERLDRERVLM DKYELKNKKE LWKHETQLKN FRRRARRLLA ARGKQAEIER EQLLARLKRL GLLPEDAVL DDVLSLTIED ILERRLQTIV YKKGLARTMR QARQLIVHGH IEVNGQIIRS PSYLVLKEEE DTITYARTSP F ANPQHPER MMIEKAKQGG EA

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #6: 30S ribosomal protein S4e

MacromoleculeName: 30S ribosomal protein S4e / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 28.246119 KDa
SequenceString: MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV ...String:
MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEEE ANIKPLRIRN KRMVKGAKIQ LNFHDGTNHL IPLSEKDNYF T SYTVLMKV PEREILEVLP FEKGAYVFVT QGKNVARKGR IVEIKKFPMG WPDVVTIEDE EGELFDTLKE YAFVVGRDKP RI SLP

UniProtKB: Small ribosomal subunit protein eS4

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Macromolecule #7: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 26.523904 KDa
SequenceString: MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG ...String:
MSQEWKEYAK RVLDEWQPKT KLGMLVKEGQ ITDIHEIFRK GYQIKEPEII DVLLPEVNAR ENQEILDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGREVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFTVEGKE GSVRVKLIPG P RGLGLVIG DVGKKILRLA GIQDVWSQTL GETRTTVNFA KAVFNALYNT NKVVVTPEMI ERYGIVVGRA MPASFTLE

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: 30S ribosomal protein S6e

MacromoleculeName: 30S ribosomal protein S6e / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 14.029461 KDa
SequenceString:
MATFKLVISD PKTGIAKQIE ITGPEAEKLI GKRIGDQIPV KELGINLNEL FGKEFPEDVK MEIRGGTDKD GFPMRPDIHG PRRVRILLS KGPGFRPKEK GERRKKTVRG NTISPEIVQV NVKLVY

UniProtKB: Small ribosomal subunit protein eS6

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Macromolecule #9: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 24.662818 KDa
SequenceString: MAKPLSERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEKRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ...String:
MAKPLSERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEKRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ASAKCYRTKM SFAEALAEEI ILAANKDPKS YAYSKKLEIE RIAESSR

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #10: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 14.772246 KDa
SequenceString:
MTLLDPLANA LSHITNSERV GKREVYIKPA SKLIGEVLRV MQKYGYIGEF EFIDDGRAGV YRVQLLGKIN KAGAIKPRFP VKARDYERW EKRFLPAFEF GILIVSTSQG VMSHKEAREK GIGGRLIAYV Y

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #11: 30S ribosomal protein S8e

MacromoleculeName: 30S ribosomal protein S8e / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 14.293733 KDa
SequenceString:
MAIWQGRSLR KPSGGRIVLA RKKRKRELGR EPSNTRVAEQ DKRKIIRTYG GNKKVRLTAA AYANVFDKSG KGRKVRIIRV IENPANRQF ARRNIITKGA IIETEIGKAK VTSRPGQDGV VNAILLEE

UniProtKB: Small ribosomal subunit protein eS8

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Macromolecule #12: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 15.293867 KDa
SequenceString:
MRIIQTTGKR KTAIARAVIR EGKGRVRING KPVELVEPEI ARFTILEPLI LAGEEIWNSV DIDVKVQGGG FMGQAEAARI AIARALVEW TGDMNLKEKF IKYDRTMLVG DPRRTEPHKP NRSTKGPRAK RQKSYR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #13: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 11.795769 KDa
SequenceString:
MQKARIKLAS TNVRSLEEVA NQIKQIAERT GVRMSGPIPL PTKRIRIVTR KSPDGEGSAT FDRWELRIHK RLIDIEADER AMRQIMRIR VPEDVTIEIE LIS

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #14: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 14.77295 KDa
SequenceString:
MSEEQVNIKK KEKWGIAHIY SSYNNTIIHI TDITGAETIS RWSGGMVVKA DRDEPSPYAA MLAARRAAEE ALEKGIVGVH IRVRAPGGS KSKTPGPGAQ AAIRALARAG LKIGRVEDVT PIPHDGTRPK GGRRGRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #15: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 16.477621 KDa
SequenceString:
MPGKKAPNGE FAGRKLKLKR KKFRWSDIRY KRRVLRLKEK SDPLEGAPQA RGIVLEKIAV EAKQPNSGMR KAVRVQLIKN GKVVTAFCP GDGAIKFIDE HDEVIIEGIG GPKGGSMGDI PGIRYKVVKV NRVSLKELVK GRKEKPRR

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #16: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 16.992912 KDa
SequenceString:
MADFRHIVRV AGVDLDGNKQ LRWALTAIKG VGINFATMVC RVAGLDPFMK AGYLTDEQVK KIEEILQDPV AHGIPRWAVN RPKDYETGR DLHLITAKLD MAIREDIMRL RRIRAYRGIR HELGLPVRGQ RTRSNFRRGQ TVGVSRKKK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #17: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 6.644064 KDa
SequenceString:
MAKADYNKRK PRKFGKGARR CIRCGQYGPI IRIHGLMLCR HCFREVAPKL GFRKYE

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #18: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 18.697143 KDa
SequenceString:
MARMHARKRG KSGSKRPPRT APPIWLEYTV EDIENLVVKL RKEGYSTAMI GTILRDQYGI PTVKLFRDPD NPNRKLTITR ILEKHGLAP EIPEDLMFLI KRAVNLRKHL EQHPKDLHSM RGLQLIESKI RRLVKYYKRK GKLPKDWRYD PEQAKLLVR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #19: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.364604 KDa
SequenceString:
MVRDIGLRIQ PPAEKCDDPK CPWHGHLKIH GRVFEGIVVS DKPRKTVTVE RQYYHYLKKY ERYELRRSRI HAHNPPCINA KVGDRVLIA ETRPLSKTKH FVVVAVLERA EERR

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #20: 30S ribosomal protein S17e

MacromoleculeName: 30S ribosomal protein S17e / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 8.059528 KDa
SequenceString:
MGKIRQGFIK RVARELFNKY PNEFTRDFEH NKKKVEELTN VTSKKIRNRI AGYITKLVRM KEEGKIL

UniProtKB: Small ribosomal subunit protein eS17

+
Macromolecule #21: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 15.307319 KDa
SequenceString:
MARKEFRYRG YTLEQLMNMS LEELAKLLPA RQRRSLKRGL TPEQKKLLRK IRLAKKGKYN KPIRTHCRDM IVLPEMVGLT IYVHNGKEF VPVEIKPEMI GHYLGEFAPT RKRVQHGAPG IGATRSSMFV AVK

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #22: 30S ribosomal protein S19e

MacromoleculeName: 30S ribosomal protein S19e / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 17.42225 KDa
SequenceString:
MATVYDVPGD LLVERVAQRL KEIPEIKPPE WAPFVKTGRH KERLPEQEDW WYYRVASILR RVYLDGPVGI ERLRTYYGGR KNRGHAPER FYKAGGSIIR KALQQLEAAG FVEKVPGKGR VITPKGRSFL DKIATELKKE LEEIIPELKK Y

UniProtKB: Small ribosomal subunit protein eS19

+
Macromolecule #23: 30S ribosomal protein S24e

MacromoleculeName: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 11.798637 KDa
SequenceString:
MEIKITEVKE NKLIGRKEIY FEIYHPGEPT PSRKDVKGKL VAMLDLNPET TVIQYIRSYF GSYKSKGYAK YYYDKDRMLY IEPEYILIR DGIIEKKEGE

UniProtKB: Small ribosomal subunit protein eS24

+
Macromolecule #24: 30S ribosomal protein S27e

MacromoleculeName: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 7.186609 KDa
SequenceString:
MALPRNVIPM PRSRFLRVKC IDCGNEQIVF SHPATRVRCN VCGATLVEPT GGKGIIRAKI LEVLE

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #25: 30S ribosomal protein S28e

MacromoleculeName: 30S ribosomal protein S28e / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 8.102305 KDa
SequenceString:
MAEDEGYPAE VIEIIGRTGT TGDVTQVKVR ILEGRDKGRV IRRNVRGPVR VGDILILRET EREAREIKSR R

UniProtKB: Small ribosomal subunit protein eS28

+
Macromolecule #26: 30S ribosomal protein S27ae

MacromoleculeName: 30S ribosomal protein S27ae / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 5.992168 KDa
SequenceString:
MGQKWKLYIV KDGKVIRKNK FCPRCGPGVF MADHGDRWAC GRCGYTEWKK K

UniProtKB: Small ribosomal subunit protein eS31

+
Macromolecule #27: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 23.472309 KDa
SequenceString: MAIERYFIRE AVKEMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE RQFGLENPQI DVQEIKNPY LNAKVQAVRI AQALERGIHF RRAAYAAMRA IMSNGARGVE IRISGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSKGYAQ ...String:
MAIERYFIRE AVKEMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE RQFGLENPQI DVQEIKNPY LNAKVQAVRI AQALERGIHF RRAAYAAMRA IMSNGARGVE IRISGKLTGE RAKSVRFYQG YLAKVGNPAE T LVSKGYAQ ALLKLGVIGV KVAIMPPDAR LPDEIEIIEK PVEEEVSSNE AE

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #28: 50S ribosomal protein L41e

MacromoleculeName: 50S ribosomal protein L41e / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Molecular weightTheoretical: 4.910237 KDa
SequenceString:
MKRRPRKWKK KGRMRWKWIK KRIRRLKRQR KKERGL

UniProtKB: Small ribosomal subunit protein eS32

+
Macromolecule #29: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.442678 KDa
SequenceString:
MAKPSYVKFE VPKELAEKAL QAVEIARDTG KIRKGTNETT KAVERGQAKL VIIAEDVDPE EIVAHLPPLC EEKEIPYIYV PSKKELGAA AGIEVAAASV AIIEPGKARD LVEEIAMKVR ELMK

UniProtKB: Large ribosomal subunit protein eL8

+
Macromolecule #32: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 32 / Number of copies: 90 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #33: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 33 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #34: water

MacromoleculeName: water / type: ligand / ID: 34 / Number of copies: 2083 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.7
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2000000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6swc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7zhg:
High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop

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