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- EMDB-10323: IC2 body cryo-EM structure of a full archaeal ribosomal translati... -

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Basic information

Entry
Database: EMDB / ID: EMD-10323
TitleIC2 body cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Map dataIC2 body map
Sample
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 body
    • Complex: ribosome
      • RNA: x 1 types
      • Protein or peptide: x 16 types
    • Complex: mRNA
      • RNA: x 1 types
    • Complex: Translation initiation factor 1A
      • Protein or peptide: x 1 types
  • Ligand: x 3 types
KeywordsTranslation initiation / cryo-EM / ribosome / tRNA / evolution / archaea / rRNA modifications
Function / homology
Function and homology information


translation initiation factor activity / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / 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 S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / 30S ribosomal protein S3Ae / : / Ribosomal protein S11, archaeal ...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 S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / 30S ribosomal protein S3Ae / : / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S8e, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 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 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 S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / 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 S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11
Similarity search - Domain/homology
Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / 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 / Translation initiation factor 1A ...Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / 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 / Translation initiation factor 1A / Small ribosomal subunit protein uS2 / 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) / Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCoureux P-D / Mechulam Y / Schmitt E
Funding support France, 1 items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0037 France
CitationJournal: Commun Biol / Year: 2020
Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
History
DepositionSep 20, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6swd
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10323.png

Downloads & links

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Map

FileDownload / File: emd_10323.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIC2 body map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 348 pix.
= 379.32 Å		1.09 Å/pix.
x 348 pix.
= 379.32 Å		1.09 Å/pix.
x 348 pix.
= 379.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.018816726 - 0.0495441
Average (Standard dev.)-0.00016238765 (±0.0019113938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 379.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z348348348
origin x/y/z0.0000.0000.000
length x/y/z379.320379.320379.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS348348348
D min/max/mean-0.0190.050-0.000

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Supplemental data

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Mask #1

Fileemd_10323_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: IC2 body postprocessed map

Fileemd_10323_additional.map
AnnotationIC2 body postprocessed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 body half1 map

Fileemd_10323_half_map_1.map
AnnotationIC2 body half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: IC2 body half2 map

Fileemd_10323_half_map_2.map
AnnotationIC2 body half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Archaeal translation initiation complex devoid of aIF1 - IC2 body

EntireName: Archaeal translation initiation complex devoid of aIF1 - IC2 body
Components
  • Complex: Archaeal translation initiation complex devoid of aIF1 - IC2 body
    • Complex: ribosome
      • RNA: 16S ribosomal RNA
      • 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 S8
      • Protein or peptide: 30S ribosomal protein S8e
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S24e
      • Protein or peptide: 30S ribosomal protein S27e
      • Protein or peptide: 30S ribosomal protein aL41
    • Complex: mRNA
      • RNA: mRNA
    • Complex: Translation initiation factor 1A
      • Protein or peptide: Translation initiation factor 1A
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2 body

SupramoleculeName: Archaeal translation initiation complex devoid of aIF1 - IC2 body
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Molecular weightTheoretical: 1.05 MDa

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Supramolecule #2: ribosome

SupramoleculeName: ribosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#17
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Supramolecule #3: mRNA

SupramoleculeName: mRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #18
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Supramolecule #4: Translation initiation factor 1A

SupramoleculeName: Translation initiation factor 1A / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #19
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 340.430125 KDa
SequenceString: AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU ...String:
AUUC(4AC)GGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC AUGCGAGUCA AGGGGGCGUC CC UUCUGGG ACGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGG GCUAAU CCCCCAUAGG CCUGGGGUAC UGGAAGGUCC CCAGGCCGAA AGGGAGCCGU AAGGCUCCGC CCGAGGAUGG GCCG GCGGC (LHH)GAUUAGGUA GUUGGUGGGG UAACGGCCCA CCAAGC(4AC)GAA GAUCGGUACG GGC(4AC)GUGAGA GCG GGAGCC (4AC)GGAGAUGGA CACUGAGACA CGGGUCCAGG CCCUACGGGG CGCAGCAGGC GCGA(A2M)ACCUC (4AC)G CAAUGCG GGAAAC(4AC)GCG ACGGGGGGAC CCCCAGUGCC GUGCCUCUGG CACGGCUUUU CCGGAGUGUA AAAAGCUCC GGGAAUAAGG GCUGGGCAAG GC(4AC)GGUGGCA GCCGCCGCGG UAAUACCGGC GGCC(4AC)GAGUG GUGGCCACUA UU AUUGGGC CUAAAGCGGC (4AC)GUAGCCGGG CCCGUAAGUC CCUGGCGAAA UCCCACGGCU CAAC(4AC)GUGGG GCUCG CUGG GGAUACUGCG GGCCUUGGGA C(4AC)GGGAGAGG C(4AC)GGGGGUAC CCC(4AC)GGGGUA GGGGUGAAAU CCUA UAAUC CCGGGGGGAC CGCCAGUGGC GAAGGCGCC(4AC) GGCUGGAACG GGUC(4AC)GACGG UGAGGGC(4AC)GA AGG CCAGGG GAGCGAAC(4AC)G GAUUAGAUAC CCGGGUAGUC CUGGCUGUAA AGGAUGCGGG CUAGGUGUCG GGCGAGCUUC GAGCUCGCC CGGUGC(4AC)GUA GGGAAGC(4AC)GU UAAGCC(4AC)GC(4AC) GCCUGGGGAG UACGGC(4AC)GCA A GGCUGAAA CUUAAAGGAA UUGGCGGGGG AGCCUGCUCC UUGCACACAC CG(OMC)C(5HM)GUCAC UCCACCCGAG CGGG GCCUA GGUGAGGCCC GAUCUCCUUC GGGAGGUCGG GUCGAGCCUA GGCUCCGUGA GGGGGGAGAA GUCG(UR3)A(6MZ) CA AGGUAGC(4AC)GU AGGGG(MA6)(MA6)CCU ACGGCUCGAU CACCUCCU

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Macromolecule #18: mRNA

MacromoleculeName: mRNA / type: rna / ID: 18 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 6.448871 KDa
SequenceString:
UGGAGGUGAU UUAAAUGCCA

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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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 (strain GE5 / Orsay) (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 S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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 #10: 30S ribosomal protein S8e

MacromoleculeName: 30S ribosomal protein S8e / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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 #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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

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Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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

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Macromolecule #13: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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

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Macromolecule #14: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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

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Macromolecule #15: 30S ribosomal protein S24e

MacromoleculeName: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (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

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Macromolecule #16: 30S ribosomal protein S27e

MacromoleculeName: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 7.186609 KDa
SequenceString:
MALPRNVIPM PRSRFLRVKC IDCGNEQIVF SHPATRVRCN VCGATLVEPT GGKGIIRAKI LEVLE

UniProtKB: Small ribosomal subunit protein eS27

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Macromolecule #17: 30S ribosomal protein aL41

MacromoleculeName: 30S ribosomal protein aL41 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 4.910237 KDa
SequenceString:
MKRRPRKWKK KGRMRWKWIK KRIRRLKRQR KKERGL

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Macromolecule #19: Translation initiation factor 1A

MacromoleculeName: Translation initiation factor 1A / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (strain GE5 / Orsay) (archaea) / Strain: GE5 / Orsay
Molecular weightTheoretical: 13.078265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPKKERKVEG DEVIRVPLPE GNQLFGVVEQ ALGAGWMDVR CEDGKIRRCR IPGKLRRRVW IRVGDLVIVQ PWPVQSDKRG DIVYRYTQT QVDWLLRKGK ITQEFLTGGS LLVE

UniProtKB: Translation initiation factor 1A

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Macromolecule #20: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 25 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #21: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 21 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #22: water

MacromoleculeName: water / type: ligand / ID: 22 / Number of copies: 26 / 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

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Sample preparation

BufferpH: 6.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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