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- EMDB-50612: PF30S-PF30S dimer mediated by aRDF from P. furiosus (Structure II) -

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Basic information

Entry
Database: EMDB / ID: EMD-50612
TitlePF30S-PF30S dimer mediated by aRDF from P. furiosus (Structure II)
Map data
Sample
  • Complex: PF30S-PF30S dimer facilitated by aRDF (Structure II)
    • Protein or peptide: x 29 types
    • RNA: x 1 types
KeywordsPyrococcus furiosus / ribosomal subunit / dimerization / anti-association / ribosome-associated protein / TRANSLATION
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 / rRNA processing / 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 / rRNA processing / 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 / 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 S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / 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 S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain
Similarity search - Domain/homology
RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 ...RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS32 / Uncharacterized protein / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS27
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHassan AH / Demo G
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLL2008 Czech Republic
European Union (EU)LX22NPO5103European Union
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.
Authors: Ahmed H Hassan / Matyas Pinkas / Chiaki Yaeshima / Sonoko Ishino / Toshio Uchiumi / Kosuke Ito / Gabriel Demo /
Abstract: Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often ...Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.
History
DepositionJun 11, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50612.png

Downloads & links

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Map

FileDownload / File: emd_50612.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 576 pix.
= 480.384 Å		0.83 Å/pix.
x 576 pix.
= 480.384 Å		0.83 Å/pix.
x 576 pix.
= 480.384 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-7.837683 - 19.619745000000002
Average (Standard dev.)0.0058524045 (±0.8484208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 480.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50612_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_50612_half_map_2.map
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Sample components

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Entire : PF30S-PF30S dimer facilitated by aRDF (Structure II)

EntireName: PF30S-PF30S dimer facilitated by aRDF (Structure II)
Components
  • Complex: PF30S-PF30S dimer facilitated by aRDF (Structure II)
    • Protein or peptide: RNA-binding protein
    • Protein or peptide: Small ribosomal subunit protein eS32
    • Protein or peptide: Archaeal Ribosome Dimerizing Factor (aRDF)
    • Protein or peptide: Large ribosomal subunit protein eL8
    • RNA: 16S rRNA
    • Protein or peptide: Small ribosomal subunit protein uS2
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: Small ribosomal subunit protein eS1
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: Small ribosomal subunit protein eS4
    • Protein or peptide: Small ribosomal subunit protein uS5
    • 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 uS14
    • Protein or peptide: Small ribosomal subunit protein uS15
    • Protein or peptide: Small ribosomal subunit protein uS17
    • 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 eS31
    • Protein or peptide: Small ribosomal subunit protein eS27
    • Protein or peptide: Small ribosomal subunit protein eS28

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Supramolecule #1: PF30S-PF30S dimer facilitated by aRDF (Structure II)

SupramoleculeName: PF30S-PF30S dimer facilitated by aRDF (Structure II) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: RNA-binding protein

MacromoleculeName: RNA-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 6.824008 KDa
SequenceString:
MVEMKFEIPV CTSCGREITP REHATHFICP NCGEAVIWRC ESCRVLAKPY KCPNCGWEGP

UniProtKB: RNA-binding protein

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Macromolecule #2: Small ribosomal subunit protein eS32

MacromoleculeName: Small ribosomal subunit protein eS32 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 5.023395 KDa
SequenceString:
MKRRPRKWKK KGRMRWKWIK KRIRRLKRQR KKERGLI

UniProtKB: Small ribosomal subunit protein eS32

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Macromolecule #3: Archaeal Ribosome Dimerizing Factor (aRDF)

MacromoleculeName: Archaeal Ribosome Dimerizing Factor (aRDF) / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 34.792625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKVVGIKGSV SYLQALKYLK TKKVTKRLKE IEKLVDTLIT LAPYAPEGSK IETIRKNYAK ISFNKIKTVS RSKIGSPRIK SIMLLLWNF GLLDVKIIEN SWYVRKTKLA SLLEENFKDL SPSEKLKVYL LGGLLVDTPA RFVYRCTLNG VEDYKGVKKA I LGYLSDQR ...String:
MKVVGIKGSV SYLQALKYLK TKKVTKRLKE IEKLVDTLIT LAPYAPEGSK IETIRKNYAK ISFNKIKTVS RSKIGSPRIK SIMLLLWNF GLLDVKIIEN SWYVRKTKLA SLLEENFKDL SPSEKLKVYL LGGLLVDTPA RFVYRCTLNG VEDYKGVKKA I LGYLSDQR SNSLIIGLSN MLESIKFIEE AQAYSGKKEY IGLVDVAFYG LSGLYLDVKR ESGKLTVKPN FRELRALYEI DK SVATGSD YGLSISKEIL ENLANTKRRK TIFSEEVQEL LVNVIKENAI SISQDLQNMY GIIHHHHHH

UniProtKB: Uncharacterized protein

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Macromolecule #4: Large ribosomal subunit protein eL8

MacromoleculeName: Large ribosomal subunit protein eL8 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 13.414664 KDa
SequenceString:
MAKPSYVKFE VPKELAEKAL QAVEIARDTG KIRKGTNETT KAVERGQAKL VIIAEDVDPE EIVAHLPPLC EEKEIPYIYV PSKKELGAA AGIEVAAASV AIIEPGKARD LVEEIAMKVK ELMK

UniProtKB: Large ribosomal subunit protein eL8

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Macromolecule #6: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 23.039861 KDa
SequenceString: MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA KFEPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVLIVTD PRADHQAMRE AVEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY ...String:
MADEYLVPLD QYLAAGVHIG TQQKTKDMKK FIYRVRQDGL YVLDVRKTDE RLKVAGKFLA KFEPQSILAV SVRLYGQKPV KKFGEVTGA RAIPGRFLPG TMTNPAVKNF FEPDVLIVTD PRADHQAMRE AVEIGIPIVA LVDTENLLSY VDLAIPTNNK G RKALALIY WILAREILYN RGEIQSREDF KIPVEEFEMK IVRR

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #7: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 23.464352 KDa
SequenceString: MAIERYFIRE AVREMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE KQFGLENPQI EVEEIKNPY LNAKVQAVRL AQALERGIHF RRAAYAALRA IMNNGARGVE IRLSGKLTGE RAKSIRFYQG YLAKVGNPAE T LVSKGYAQ ...String:
MAIERYFIRE AVREMLIDEF LEKELRRAGY GGLDIKKTPL GTKVIIFAAN PGYVIGRGGR RIRELTRILE KQFGLENPQI EVEEIKNPY LNAKVQAVRL AQALERGIHF RRAAYAALRA IMNNGARGVE IRLSGKLTGE RAKSIRFYQG YLAKVGNPAE T LVSKGYAQ ALLKLGVIGV KVAIMPPGAR LPDEIEIIEK PVEEEVVSNE AE

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #8: Small ribosomal subunit protein eS1

MacromoleculeName: Small ribosomal subunit protein eS1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 22.984107 KDa
SequenceString: MAAKRATTTR DKWKLKQWYI IYAPDFFGGV EVGLTPADDP EKVLNRVVEV TLKDVTGDFT KSHVKLYFQV YDVKGQNAYT KFKGMKLAR SYIRSLVRRK TTRIDGIFNI TTKDGYKLRV MAMAIAMRRI QTSQERAIRK IMQEIIYKKA EELNFKDFVL E SVNGKIAA ...String:
MAAKRATTTR DKWKLKQWYI IYAPDFFGGV EVGLTPADDP EKVLNRVVEV TLKDVTGDFT KSHVKLYFQV YDVKGQNAYT KFKGMKLAR SYIRSLVRRK TTRIDGIFNI TTKDGYKLRV MAMAIAMRRI QTSQERAIRK IMQEIIYKKA EELNFKDFVL E SVNGKIAA EIAKEAKKIY PLRKAEIRKI KVLEEPQVIA

UniProtKB: Small ribosomal subunit protein eS1

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Macromolecule #9: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
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 #10: Small ribosomal subunit protein eS4

MacromoleculeName: Small ribosomal subunit protein eS4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 28.197023 KDa
SequenceString: MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEDE AFIKPLRIRN KRMIKGARVQ LNFHDGTNHI VSIAEKDNYF T SYTVLMKV ...String:
MARKGPKRHL KRLAAPTSWY IERKAYKWAV RPRPGPHNMR TSIPLLYIVR DYLGYAKTAR EARKILNEGK FLVDGRVRKD YKFPVGIMD VVSIPETGEH YRVLPNRIGK LILHPISEDE AFIKPLRIRN KRMIKGARVQ LNFHDGTNHI VSIAEKDNYF T SYTVLMKV PEREILEVLP FEKGAYVFVT QGKNVARKGR IVEIKRFPMG WPDVVTIEDE EGELFDTLKE YAFVVGTDKP KI SLP

UniProtKB: Small ribosomal subunit protein eS4

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Macromolecule #11: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 26.590891 KDa
SequenceString: MSQEWKEYAK RVLDEWEPKT KLGMMVKEGQ ITDIHEIFRR GYQIKEPEII DVLLPEVNAR ENQEVLDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGKEVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFAVEGKE GSVRVRLIPG P RGLGLVIG ...String:
MSQEWKEYAK RVLDEWEPKT KLGMMVKEGQ ITDIHEIFRR GYQIKEPEII DVLLPEVNAR ENQEVLDIAL TVRMTDSGRR VRFRVLAAV GNRDGYVGLG IGHGKEVGIA IRKAINYAKL NIIEIKRGCG SWECRCRRPH SVPFAVEGKE GSVRVRLIPG P RGLGLVIG DVGKKILRLA GVQDVWSQTF GETRTTVNFA KAVFNALYNT NRVAISPEMI ERYGIVVGRA MPTTFTLE

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #12: Small ribosomal subunit protein eS6

MacromoleculeName: Small ribosomal subunit protein eS6 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 14.00233 KDa
SequenceString:
MATFKLVISD PKSGIAKQVE ITGAETEKLI GKRIGDQIPA KELNINLNEL FGKEFPEDVK LEIRGGTDKD GFPMRPDIHG PRRVRVLLS KGPGFRPKEK GERRKKTVRG NTISPEIVQV NVKLVY

UniProtKB: Small ribosomal subunit protein eS6

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Macromolecule #13: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 24.701791 KDa
SequenceString: MAKPLNERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEQRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ...String:
MAKPLNERFF IPHEIKVMGR WSTEDVEVRD PSLKPYINLE PRLLPHTHGR HAKKHFGKAN VHIVERLINK IMRSGGSHYK VAGHFMRRE HRSLNSKKVK AYEVVKEAFK IIEQRTGKNP IQVLVWAIEN AAPREDTTSV MFGGIRYHVA VDISPMRRLD V ALRNIALG ASAKCYRNKM SFAEALAEEI ILAANKDPKS YAYSKKLEIE RIAESSR

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #14: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 14.684174 KDa
SequenceString:
MTLLDPLANA LSHITNSERV GKREVYIKPA SKLIGEVLRV MQKYGYIGEF EFIDDGRAGV YRVQLLGRIN KAGAIKPRFP VKVSEFEKW EKRFLPAFEF GILIVSTSQG VMSHKEAIEK GIGGRLIAYV Y

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #15: Small ribosomal subunit protein eS8

MacromoleculeName: Small ribosomal subunit protein eS8 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 14.293733 KDa
SequenceString:
MAIWQGRSLK KPSGGRIVLA RKKRKRELGR EPSNTRVAEQ DKRKIIRTYG GNRKVRLTAA AYANVFDKSG KGRKVRIIRV IENPANRQF ARRNIITKGA IIETEIGKAK VTSRPGQDGV VNAILLEE

UniProtKB: Small ribosomal subunit protein eS8

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Macromolecule #16: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 15.317932 KDa
SequenceString:
MRIIQTTGKR KTAIARAVIR EGKGRVRING KPVEIIEPEI ARFTILEPLI LAGEEIWNSV DIDVKVEGGG FMGQAEAARM AIARALVEW TGDMSLKEKF MKYDRTMLVG DPRRTEPHKP NRSTKGPRAK RQKSYR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #17: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 11.769689 KDa
SequenceString:
MQKARIKIAS TNVRSLDEVA NQIKQIAERT GVRMSGPIPL PTKRIRITTR KSPDGEGSAT FDRWELRVHK RLIDIEADER AMRQIMRIR VPEDVTIEIE LIS

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #18: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 14.75695 KDa
SequenceString:
MSEEQVNIKK KEKWGIAHIY SSFNNTIIHI TDITGAETIS RWSGGMVVKA DRDEPSPYAA MLAARRAAEE ALEKGIVGVH IRVRAPGGS KSKTPGPGAQ AAIRALARAG LKIGRVEDVT PIPHDGTRPK GGRRGRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #19: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
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 #20: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 16.948904 KDa
SequenceString:
MANFRHIVRV AGVDLDGNKQ LRWALTAIKG IGINFATMVC RVAGLDPFMK AGYLTDEQVK KIEEILADPV AHGIPRWAVN RPKDYETGR DLHLITAKLD MAIREDIMRL RRIRAYRGIR HELGLPVRGQ RTRSNFRRGQ TVGVSRKKK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #21: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 6.634046 KDa
SequenceString:
MAKADYNKRK PRKFGKGARR CIRCGQYGPI IRIQGLMLCR HCFREVAPKL GFRKYE

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #22: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 18.640025 KDa
SequenceString:
MARMHARKRG KSGSKRPPRT APPIWVEYTV EEIENLVVKL RKEGYSTAMI GTILRDQYGI PSVKLFKDPD NPNRNLTITR ILEKHGLAP EIPEDLMFLI RRAVNLRKHL EQHPKDLHSM RGLQLIESKI RRLVKYYKRK GKLPKNWRYD PETAKLLVR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #23: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 13.296521 KDa
SequenceString:
MMRDIGLRVQ PPAEKCDDPK CPWHGNLKIH GRVFEGIVVS DKPRKTVTVE RQYYFYLNKY ERYELRRSKI HAHNPPCINA KVGDKVLIA ETRPLSKTKH FVVVAVLERA EERR

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #24: Small ribosomal subunit protein eS17

MacromoleculeName: Small ribosomal subunit protein eS17 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 7.942465 KDa
SequenceString:
MGKIRQGFIK RVARELVNKY PNEFTTDFEH NKKKVQELTN VTSKKIRNRI AGYVTKLVRM KMEGKIL

UniProtKB: Small ribosomal subunit protein eS17

+
Macromolecule #25: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 15.357399 KDa
SequenceString:
MARKEFRYRG YTLEQLMNMS LEELARLFPA RQRRSLKRGL TPEQKKLLRK IRLAKKGKYK KPIRTHCRDM IILPEMVGLT IYVHNGKEF VPVEIKPEMI GHYLGEFAPT RKKVEHGAPG VGATRSSMFV AVK

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #26: Small ribosomal subunit protein eS19

MacromoleculeName: Small ribosomal subunit protein eS19 / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 17.394236 KDa
SequenceString:
MATVYDVPGD LLVERVAQRL KEIPEIKPPE WAPFVKTGRH KERLPEQEDW WYYRVASILR RVYLDGPVGI ERLRTYYGGR KNRGHAPEK FYKAGGSIIR KALQQLEAAG FVEKVPGKGR VITPKGRSFL DKIATELKKE LEEIIPELKK Y

UniProtKB: Small ribosomal subunit protein eS19

+
Macromolecule #27: Small ribosomal subunit protein eS24

MacromoleculeName: Small ribosomal subunit protein eS24 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 11.698564 KDa
SequenceString:
MEIRIKEIKE NKLIGRKEIY FEIYHPGEPT PSRKDVKGKL VAMLDLNPET TVIQYIRSYF GSYISKGYAK AYDSKERMLY IEPEYILIR DGLIEKKEGE

UniProtKB: Small ribosomal subunit protein eS24

+
Macromolecule #28: Small ribosomal subunit protein eS31

MacromoleculeName: Small ribosomal subunit protein eS31 / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 5.864958 KDa
SequenceString:
MGQKWKLYEI KDGKVIRKNK FCPRCGPGVF MADHGDRWAC GKCGYTEWKK

UniProtKB: Small ribosomal subunit protein eS31

+
Macromolecule #29: Small ribosomal subunit protein eS27

MacromoleculeName: Small ribosomal subunit protein eS27 / type: protein_or_peptide / ID: 29 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 6.888388 KDa
SequenceString:
MAKPIIPMPR SRFLRVKCID CGNEQIVFSH PATKVRCLIC GATLVEPTGG KGIVKAKILE VLE

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #30: Small ribosomal subunit protein eS28

MacromoleculeName: Small ribosomal subunit protein eS28 / type: protein_or_peptide / ID: 30 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 8.116332 KDa
SequenceString:
MAEDEGYPAE VIEIIGRTGT TGDVTQVKVR ILEGRDKGRV IRRNVRGPVR IGDILILRET EREAREIKSR R

UniProtKB: Small ribosomal subunit protein eS28

+
Macromolecule #5: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 5 / Number of copies: 2
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 485.4555 KDa
SequenceString: AUUCCGGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC CGACUAAGCC AUGCGAGUCA AGGGGGCGUC CCUUCUGGGA CGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGGGCUAAUC C CCCAUAGG ...String:
AUUCCGGUUG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC CGACUAAGCC AUGCGAGUCA AGGGGGCGUC CCUUCUGGGA CGCCACCGG CGGACGGCUC AGUAACACGU CGGUAACCUA CCCUCGGGAG GGGGAUAACC CCGGGAAACU GGGGCUAAUC C CCCAUAGG CCUGGGGUAC UGGAAGGUCC CCAGGCCGAA AGGGAGCCGU AAGGCCCGCC CGAGGAUGCG GCGGCGGCCG AU UAGGUAG UUGGUGGGGU AACGGCCCAC CAAGCCGAAG AUCGGUACGG GCCGUGAGAG CGGGAGCCCG GAGAUGGACA CUG AGACAC GGGUCCAGGC CCUACGGGGC GCAGCAGGCG CGAAACCUCC GCAAUGCGGG AAACCGCGAC GGGGGGACCC CCAG UGCCG UGCCUCUGGC ACGGCUUUUC CGGAGUGUAA AAAGCUCCGG GAAUAAGGGC UGGGCAAGGC CGGUGGCAGC CGCCG CGGU AAUACCGGCG GCCCGAGUGG UGGCCACUAU UAUUGGGCCU AAAGCGGCCG UAGCCGGGCC CGUAAGUCCC UGGCGA AAU CCCACGGCUC AACCGUGGGG CUCGCUGGGG AUACUGCGGG CCUUGGGACC GGGAGAGGCC GGGGGUACCC CCGGGGU AG GGGUGAAAUC CUAUAAUCCC GGGGGGACCG CCAGUGGCGA AGGCGCCCGG CUGGAACGGG UCCGACGGUG AGCGCGGA A GGCCAGGGGA GCGAACCGGA UUAGAUACCC GGGUAGUCCU GGCUGUAAAG GAUGCGGGCU AGGUGUCGGG CGAGCUUCG AGCUCGCCCG GUGCCGUAGG GAAGCCGUUA AGCCCGCCGC CUGGGGAGUA CGGCCGCAAG GCUGAAACUU AAAGGAAUUG GCGGGGGAG CACUACAAGG GGUGGAGCGU GCGGUUUAAU UGGAUUCAAC GCCGGGAACC UCACCGGGGG CGACGGCAGG A UGAAGGCC AGGCUGAAGG UCUUGCCGGA CGCGCCGAGA GGAGGUGCAU GGCCGCCGUC AGCUCGUACC GUGAGGCGUC CA CUUAAGU GUGGUAACGA GCGAGACCCG CGCCCCCAGU UGCCAGUCCC UCCCGCUCGG GAGGAGGCAC UCUGGGGGGA CUG CCGGCG AUAAGCCGGA GGAAGGGGCG GGCGACGGUA GGUCAGUAUG CCCCGAAACC CCCGGGCUAC ACGCGCGCUA CAAU GGGCG GGACAAUGGG ACCCGACCUC GAAAGGGGAA GGGAAUCCCC UAAACCCGCC CUCAGUUCGG AUCGCGGGCU GCAAC UCGC CCGCGUGAAG CUGGAAUCCC UAGUACCCGC GUGUCAUCAU CGCGCGGCGA AUACGUCCCU GCUCCUUGCA CACACC GCC CGUCACUCCA CCCGAGCGGA GUCCGGGUGA GGCCUGAUCU CCUUCGGGAG GUCAGGUCGA GCCCGGGCUC CGUGAGG GG GGAGAAGUCG UAACAAGGUA ACCGUAGGGG AACCUACGGC UCGAUCACCU CCU

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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: 7
Component:
ConcentrationFormulaName
20.0 mMHEPES-KOHHEPES-KOH
12.0 mMMgCl2magnesium chloride
100.0 mMNH4Clamonium chloride
0.5 mMEDTAEDTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.6 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11033 / 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: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 792586
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v6u

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 63890
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 6 / Software - Name: FREALIGN (ver. 9.11)

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Atomic model buiding 1

Initial model
PDB IDChain

4v6u

source_name: PDB, initial_model_type: experimental model

7zhg

source_name: PDB, initial_model_type: experimental model
source_name: ITasser, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9fnz:
PF30S-PF30S dimer mediated by aRDF from P. furiosus (Structure II)

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