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- EMDB-49734: Methanosarcina acetivorans 50S subunit obtained from acetate-grow... -

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Basic information

Entry
Database: EMDB / ID: EMD-49734
TitleMethanosarcina acetivorans 50S subunit obtained from acetate-grown cells
Map data
Sample
  • Complex: Methanosarcina acetivorans 50S subunit obtained from acetate-grown cells
    • RNA: x 2 types
    • Protein or peptide: x 30 types
  • Ligand: x 2 types
KeywordsArchaea / Methanosarcina acetivorans / Large subunit / 50S subunit / growth conditions / acetate / RIBOSOME
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea ...Ribosomal protein L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / Ribosomal protein L7Ae, archaea / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal L40e family / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L18e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L15e, conserved site / Ribosomal protein L15e signature. / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L24e-related / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L24e / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL15 ...Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsGhosh A / Fordjour GNR / Armache J-P / Ferry JG / Murakami KS / Bevilacqua PC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM156623 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127064 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM149417 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.
Authors: George N R Fordjour / Anwesha Ghosh / James G Ferry / Jean-Paul Armache / Philip C Bevilacqua / Katsuhiko S Murakami /
Abstract: Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements ...Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on nonmethanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader Archaea domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon. Compared to ribosomes from extremophiles, the M. acetivorans ribosome has a simplified architecture, lacking paralogous duplications and containing a reduced complement of ribosomal proteins. Structures of the large subunit (50S) from cells grown with either methanol or acetate show conserved rRNA folding and protein composition. High-resolution structures of the 50S subunit from the two growth substrates enabled us to investigate structural properties that may influence in vivo dimethyl sulfate reactivity, an orthogonal chemical approach used to probe RNA structure. We observed good agreement between in vivo dimethyl sulfate reactivity and ribosome structure. Finally, we identify a previously uncharacterized ribosome dimerization mode involving only 50S subunits and mediated by a heterotetrameric complex of PurH and aEF2-proteins with alternative metabolic and translational roles. This macromolecular assembly, which we term the methanogen ribosome dimerization factor, likely mediates ribosome hibernation, revealing an alternative regulatory mechanism in translation.
History
DepositionMar 14, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49734.png

Downloads & links

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Map

FileDownload / File: emd_49734.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram (log scale)
Contour LevelBy EMDB: 0.075
Minimum - Maximum-0.425661 - 0.78954333
Average (Standard dev.)0.0009648152 (±0.020353513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49734_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_49734_half_map_2.map
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Sample components

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Entire : Methanosarcina acetivorans 50S subunit obtained from acetate-grow...

EntireName: Methanosarcina acetivorans 50S subunit obtained from acetate-grown cells
Components
  • Complex: Methanosarcina acetivorans 50S subunit obtained from acetate-grown cells
    • RNA: 23S rRNA
    • RNA: 5S rRNA
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein eL8
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein eL15
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein eL18
    • Protein or peptide: Large ribosomal subunit protein eL19
    • Protein or peptide: Large ribosomal subunit protein eL20
    • Protein or peptide: Large ribosomal subunit protein eL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: Large ribosomal subunit protein eL24
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein eL30
    • Protein or peptide: Large ribosomal subunit protein eL31
    • Protein or peptide: Large ribosomal subunit protein eL32
    • Protein or peptide: Large ribosomal subunit protein eL43
    • Protein or peptide: Large ribosomal subunit protein eL37
    • Protein or peptide: Large ribosomal subunit protein eL39
    • Protein or peptide: Large ribosomal subunit protein eL40
    • Protein or peptide: Large ribosomal subunit protein eL42
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Methanosarcina acetivorans 50S subunit obtained from acetate-grow...

SupramoleculeName: Methanosarcina acetivorans 50S subunit obtained from acetate-grown cells
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Methanosarcina acetivorans (archaea)

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1
Details: Contains an rRNA modifications: G7M2251, OMU2563 and OMG2564
Number of copies: 1
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 937.71075 KDa
SequenceString: AGGAAUUAUG CUAUCAGGUG GAUGGCUCGG CUCAAGAGCU UAUGAAGGAC GUGCCAAGCU GCGAUAAGCC CGGGGUAGGU GCAUGGAGC CAAUGAACCC GGGAUUUCCG AAUGGGACCU CUCCGUAGUG AUCAUUCAUG AUCGGGAACG CUCCGAAUUG A AACAUCUC ...String:
AGGAAUUAUG CUAUCAGGUG GAUGGCUCGG CUCAAGAGCU UAUGAAGGAC GUGCCAAGCU GCGAUAAGCC CGGGGUAGGU GCAUGGAGC CAAUGAACCC GGGAUUUCCG AAUGGGACCU CUCCGUAGUG AUCAUUCAUG AUCGGGAACG CUCCGAAUUG A AACAUCUC AGUAGGAGCG GGAAAAGAAA UCAAUUGAGA UGCCGUAAGU AACGGCGAGU GAAACCGGCA CAGUUCAAAC CG AAUCCCU UCGGGGACAU GUGGUGUUGU AGGGCUGUUC AAACGUCUGG CGGUAAAAUC GAACUUGCCU GGAACGGCAG ACC AUAGAG UGUGACAGUC ACUUAGAUGU ACGCCAAAAG ACCGGAACAU GUCCCUGAGU ACCGUGCGUU GGAUAUCGUG CGUG AAUCU GGGGGGCACC AACCUCCAAA ACUAAAUACU CCUUGAGACC GAUAGCGAAA UAGUAGGGUG ACCGAACGCU GAAAA GUAC CCCGAGAAGG GAGGUGCAAA GUGCCUGAAA CCUGAUAGUG AUGGAACGAU ACGGCAUGAA AGGAUCUCUG GCAUGA AGG AAUCAUUCGC GAGGAUGUAG UACGAAUGUC ACUGCCAGUG UCGUAUCUUA CGUUUUGAAG AACGGGCCAG GGAGUGU AU CUUGGUGGCA AUGGCUAACC UUUUAUCUGG GCAGCCGAAG CGAAAGCAAC AUGUGCGCAG CCUUUUGGCG AGGCACGA C GUAUACAAGU GCGUGGAGUC ACCGGGGUAC GACCCGAAGC CGGGUGAUCU AGGCGUGGGC AGGUUGAAGC GUGGCGAAA GCUACGUGGA GGACCGUAAA CGGUAUUGAU CUGCAAAUCA UUCGUGUGAC CUGCGUCUCG UAGUGAAAUG CUAAUCUAAC CCGGCAUCC GCUGGUUCCU UCCGAAACAU GUCGCAGCAU GACCUGACUU GAGAUCGUCG GUGGAGUAGA GCACUGAUUG G CGAUUCCG GGGGAGAAAU CCCUCGCUCG CUUGUCAAAC UCCAAACCCC CCGUCAUCCU AGAAAGUCGG AGUCCGGACU GC UGGGGUA AGCUUGUAGU CCGUAAGGGA GACAACCCAG CCCGUGGUUA AGGUCCCCAA GUGUCGACUA AGUGUUAAUA CUA AAGGGC GUCCCAAGCC CCAGACAGCU GGAAGGUUAG CUUAGAAGCA GCUACCCUUC AAAGAGUGCG UAACAGCUCA CCAG UCGAG GUUUGGGGCC CCGAAAAUUG ACGGGGCUCA AGUCGACCAC CGAUACCACG GAGUACCGCA AGGUAAUCUC GUAGG AAGG CGUUGUGUUC GGGUCGAAGC AGGGCUGUGA AGUCCUGUGG ACCGUUCACA AACGAAAAUC CUGGUAAUAG UAGCAG CAA AGCAGGGUGA GACUCCCUGC CGCCGAAGGG GCCAGGUUUC CUCGGCAAUG UUCGUCAGCC GAGGGUUAGU CGGUCCU AA GACGUACCGU AAUUCGAGUA CGCCGAAAGG GAAACAGGUU AAUAUUCCUG UACCAUUUAG CGUUUAGUCU GACGUCUC A GGGCAAGCCG AGCGGCGUCG UCGCGCCGUC UAAGCAGCGA ACCCCGUGGA GAGCCGUAAU GGCGAGAAGC GGGCGAAUC UGUAAUGGCA CAAGUCGGCU UCACCCCGGG ACCCGUGAAA AGGACAGCUA AAUGUCCGUA CCGAGAACUG ACACAGGUGC CCCUAGCUG AAAAGGCUAA GGCGUGUCGG AGUAAUUCAG UUAAGGGAAU UCGGCAAAUU AGCUCCGUAA CUUCGGGAUA A GGAGUGCC UGCUGUGUAG ACAGCAGGUC GCAGUGACCA GGGGGCUCUA ACUGUCUAAU ACCAACAUAG GAGAUUGCAA AC CCGUAAG GGCUAGUACA AUCUCUGAAU CCUGCUCAGU GCAGGUACCU GAAACCCCGG UUCAACGGGA AGAAGGGCCU GUA AACAGC GGGGGUAACU AUGACCCUCU UAAGGUAGCG UAGUACCUUG UCGCUUAAUU GGCGACUUGC AUGAAUGGAU CAAU GAGAG CCCUACUGUC CCUAACUGGA GUCCGGUGAA GCUUACAUUC UAGUGCACAG UCUAGAGACC UCUAGGGGGA AGUGA AGAC CCCGUGGAGC UUUACUGCAG CCUGUCGUUG GGUUGUGGUU CUGGAUGUAC AGUGUAGGUA GGAGGCAUCG AAGCGG GUG CGCCAGCAUU CGUGGAGCCG UCCUUGGGAC ACUACCCUUC CGGGACUACG ACCCUAACUC UGAGAAGAGG ACCCCGA UA GGUGGGCA(G7M)U UUGCCUGGGG CGGGACGCCC UUGAAAAGAU AUCAAGGGCG CGCAAUGGUU GACUCAAGCG GGUC GGAAA CUCGCUGAAG AGUGCAAGAG CAUAAGUCAG CCUGACGUUA UUCAGCAUAG CAGUGGAUGA CGAGACGAAA GUCGG CUCU AGCGAACUUU UGAGCCUCCU UGGUGGGGGC CAAAAAUGAC AGAAAAGUUA CCCCGGGGAU AAUUGAGUCG UUGCCG GCA AGAGUACAUA UCGACCCGGC AGCUUGCUAC CUCGAUGUCG GUUCUUUCCA UCCUGGCCGU GCAGCAGCGG CCAAGGG UG AGGU(OMU)(OMG)UUCG CCUAUUAAAG GAGAUCGUGA GCUGGGUUUA GACCGUCGUG AGACAGGUCG GUUACUAUCU ACUAGAGGU GCCCGAGGUC UGCGGGUAAG CUGCUUUUAG UACGAGAGGA ACCAAGCAGC GGCGCCACUG GUGUACCGGU U GUCUGACA AGGCAUCGCC GGGCAGCUAC GCGCUCAGGA AUAAGAGCUG AAUGCAUCUA AGCUCGAACU CUGACCUAAA AA GAGACCU CUUUAAGGAU UCCGGUAAAA GACCGGUUUG AUAGAAACGG GAUGUAAGCA CCAAGGCAAC GAGGUGUUCA GUC CGCGUU UACUAACCAU UCGUUCCUUU CACUU

GENBANK: GENBANK: AE010299.1

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Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 41.399551 KDa
SequenceString:
GAGUUUGGCG GCCAUAGCGG UAGGGCAACU CCUGUACCCA UCCCGAACAC AGCAGAUAAG CCUGCCCGCG UUCCUUACUG UACUGAAGU GUGCGAGCCU UCGGGAACUC UGGAUCGCUG CCAAGCUCAC

GENBANK: GENBANK: AE010299.1

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Macromolecule #3: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 25.738627 KDa
SequenceString: MGKRLISQNR GRGTPTYRAP SHKYKADLRH PRVDENSSLR GEVVGIEHDP ARSAPIAKVA FENGEELFLL ASEGIAVGNI IECGDDAEV KPGNIVPIGN VPEGFFICNV ESKPNDGGKF VRSSGVYATV VTHEATRTAV SMPSGNIKWL NPKCRAVVGI V AGSGRVDR ...String:
MGKRLISQNR GRGTPTYRAP SHKYKADLRH PRVDENSSLR GEVVGIEHDP ARSAPIAKVA FENGEELFLL ASEGIAVGNI IECGDDAEV KPGNIVPIGN VPEGFFICNV ESKPNDGGKF VRSSGVYATV VTHEATRTAV SMPSGNIKWL NPKCRAVVGI V AGSGRVDR PWLKAGKKYH KMKTRAAKYP RVSAVAMNPR DHPFGGGAWK HPGKPTTVSR NAPPGRKVGL IAARRTGMKR

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #4: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 36.949645 KDa
SequenceString: MASIHRPKRG SLAFSPRKRA KSHIPRFRAW PEATGEPKLQ SFAGYKVGMT HVIMVDDTKN SLTQGMEISV PVTVIETPAI RVAAIRAYA EDSTGEKAIA EVWAADLDPE LKRRIPIPAA GNQAEALENI GKLIEEGRVS DVRAVIYTLP KSLTGVPKKV P DIMESGIS ...String:
MASIHRPKRG SLAFSPRKRA KSHIPRFRAW PEATGEPKLQ SFAGYKVGMT HVIMVDDTKN SLTQGMEISV PVTVIETPAI RVAAIRAYA EDSTGEKAIA EVWAADLDPE LKRRIPIPAA GNQAEALENI GKLIEEGRVS DVRAVIYTLP KSLTGVPKKV P DIMESGIS ARDLGTKFEY SKTILGTLVS VTDVFKNGTL VDTAAITIGK GTQGPVKRWG IQLMKGKHSR QGSLRQVGTL GA FNPSRVS WRVPQMGQMG YHQRTEFNKR ILKIGSDGEE VTPEGGFINY GLVRGDYILI KGSVPGPSKR LIRLRDPIRA KKA DLGEPN ILYISRESKQ G

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #5: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 27.51657 KDa
SequenceString: MATAKTIDLT GKAVGEVELP AVFDADYRPD LIKKAVLAAQ ANRLQPYGPR LYSGMETSAR GWGSGRGVSH VPRLVNSSRA ARVPHAKGG RRAHPPKPEA DRSEKVNTKE RRYAIRSAIA ATTDPTLVSL RGHIFEAELP IVAVNDLESL ERTKQVIEFL E AAGLYEDV ...String:
MATAKTIDLT GKAVGEVELP AVFDADYRPD LIKKAVLAAQ ANRLQPYGPR LYSGMETSAR GWGSGRGVSH VPRLVNSSRA ARVPHAKGG RRAHPPKPEA DRSEKVNTKE RRYAIRSAIA ATTDPTLVSL RGHIFEAELP IVAVNDLESL ERTKQVIEFL E AAGLYEDV LRAKYGRHIR AGRGKLRGRK YKHKKSVLIV AGENTPILKA ARNLSGVDVV TVDSLNAELL APGTHAGRLT VW TESAIGK LEGAFQ

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #6: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 18.398299 KDa
SequenceString:
MRTPIVEKVI VHMGVGESGQ HLVNAEDILR NITGQEVVRC FAKRTLPAFS IKKNEPIGCK VTLRGQKAQE FLETALGIVE KTLNRSQFD SFGNVSFGIE EHTDFPGMRY DPNIGVFGMD VTVVLKRPGE RICKRRIAAR KIPAGHRVTV DDAIAFLNES Y GVEVM

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #7: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 19.530715 KDa
SequenceString:
MVKEIARTIE IPEGVSVSLA QDVFTATGPK GTVERKLWYP GIMIDVKDGE VVVDAEYARK EQKAMVGTFA SHIRNLVKGV NEGFECKMS IVYAHFPMQV KVDGKTLIIG NFLGEKKPRF AKIIGETKVK VSGNDVTITG INKEDVGQTA ANIEQKTKIK R FDPRIFQD GIYIVQKA

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #8: Large ribosomal subunit protein eL8

MacromoleculeName: Large ribosomal subunit protein eL8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 12.741726 KDa
SequenceString:
MAQLAKFDVP EELTNKALEA LELARDTGKI KKGTNEATKA IERGNAKLVL IAEDIEPAEI VAHIGPLSEE KKAPYIFIKN QKELGAASG LGVSCATVAI VDAGKAAEMV QDIAQKLEAL K

UniProtKB: Large ribosomal subunit protein eL8

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Macromolecule #9: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 19.409648 KDa
SequenceString:
MVRKPGSMYR NVRQRSFTRR KYMGGVPGSQ VIHYDMGDKA NTSFPVKISL IVEEKCQIRH TALEAARITA NRHLVADTGK MGFYMKLRV YPHEVIRENK QATGAGADRV SSGMRRAFGK NVGTAARVKP MQKIFTVAVE KQNFKAAKEA LWHAGQKLPT P CRIVVDEG AELVQ

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #10: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 16.085799 KDa
SequenceString:
MLKMTVIDAK GLILGRLASS VAKQLLSGDE KVYIINAEQA IISGSRAATL REYRETRERG ATEFGPYFPK RPDRILKRTI RGMLPYKRA RGRDAMSRLK VYVGVPYELK GAETVTIPDA DMRLLSSSRY VELGEVSQKM GSKF

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #11: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 14.356907 KDa
SequenceString:
MKGMRSNIPR ALNAGAQIAC VDNTGAKVVE IISVKKYRGV KNRMPCAGIG DMCVVSVKKG TPEMRKQVLL AVVVRQKQEF RRPDGLHVS FEDNAMVITD EEGIPKGTDI KGPVAREVAE RFPKIGTTAS IIV

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #12: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 15.129009 KDa
SequenceString:
MDTKKFRGSR TCGGGTHKNR RGAGNRGGRG KAGGCKHHFV RAMMRGYSYG KHGFKRPDEV SRDVSIVNVG ELDELASYLV EEGLAEVKD GAYHINLENL GIEKVLGSGR VTKNLVVTSE EFSASAREKI ENAGGSCIDA E

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #13: Large ribosomal subunit protein eL15

MacromoleculeName: Large ribosomal subunit protein eL15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 22.650105 KDa
SequenceString: MVKSFYGYVR DAWKNPDETY VNELRWERLQ VWRKQGSVTR IERPTRIDRA RSLGYKAKQG IVVVRVNVRR GGLGHVRPNR GRRTQKMGK NKVSGGMSIQ RIAEVRADRR YPNLEVLNSY WVGEDGKHKW FEVILVDPHH PVIKSDKNLN WVCDPSSRGR A TRGKTSAG ...String:
MVKSFYGYVR DAWKNPDETY VNELRWERLQ VWRKQGSVTR IERPTRIDRA RSLGYKAKQG IVVVRVNVRR GGLGHVRPNR GRRTQKMGK NKVSGGMSIQ RIAEVRADRR YPNLEVLNSY WVGEDGKHKW FEVILVDPHH PVIKSDKNLN WVCDPSSRGR A TRGKTSAG RKGRGMATRG KGTEKTRPSI RAYKSRGK

UniProtKB: Large ribosomal subunit protein eL15

+
Macromolecule #14: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 19.233713 KDa
SequenceString:
MATGPRYKVP FRRRREGRTN YHLRLKLLLS RQDRVVVRKS SRNVQIQLIA PTPDGDITYS SAVSNELAKY GYTGATGNTT AAYLTGLLF GLKSLQKGYE GGILDIGLQA SSAGSRVYAA LKGVVDSGFE IPCSPEVFPP DERIRGEHIA GYREESSDLP E QFEATKEK IFAEFS

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #15: Large ribosomal subunit protein eL18

MacromoleculeName: Large ribosomal subunit protein eL18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 13.714989 KDa
SequenceString:
MGKKSLVKLT RKTNPRIVSL ILTLKERANG DSAPIWKDIA KRLEAPSRNY AAVNISKINR HTAEDDVLLI PGKVLGAGLL DHPVTIAAL TFSDSAFEKI TEAGGKCLSL EEIMEANPKG SGIRIFR

UniProtKB: Large ribosomal subunit protein eL18

+
Macromolecule #16: Large ribosomal subunit protein eL19

MacromoleculeName: Large ribosomal subunit protein eL19 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 17.061982 KDa
SequenceString:
MSDLSNQRKL ASKVLGCGLD RVWLNPEASE EIASAITRED IRGLIEEGTI KAKPVKGVSR GRARALAAKR KYGHCKGHGS RKGKKGART PKKEQWIKKI RALRRRLKEL RADGALDKSV YCRLYRKAKG GEYRSVSHLN SHLESEKLLK KE

UniProtKB: Large ribosomal subunit protein eL19

+
Macromolecule #17: Large ribosomal subunit protein eL20

MacromoleculeName: Large ribosomal subunit protein eL20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 6.972045 KDa
SequenceString:
MVMMKSFIVK GKFKAGSTWE KFTKKIESQN EKNATDKTYS IFGSKHGVKR SQVQIESVAE E

UniProtKB: Large ribosomal subunit protein eL20

+
Macromolecule #18: Large ribosomal subunit protein eL21

MacromoleculeName: Large ribosomal subunit protein eL21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 11.06372 KDa
SequenceString:
MTNSHGEKRC TRYKLQKTVR ERGISPVSRA IQEFEEGQMV HIDIDPSVQK GMPNPKFQGS TGKVIGQRGR SYVLEVRSGN AMKEVFSLP QHLKPQKY

UniProtKB: Large ribosomal subunit protein eL21

+
Macromolecule #19: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 16.764578 KDa
SequenceString:
MARINYSING DPETTSKAMG SELHISPKKS REVCCKIKGM KASEARKFLE DVIAMKQAVP FKKHHDGSGH RKGPMAAGKY PISASKEIL KVLKNAESNA EYKGLEPANM YIIHAAIQRG RVIHGFMPRA RGRATPKDTE TVNIEMILSE VR

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #20: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 9.447194 KDa
SequenceString:
MSSINYPFVT EKAMMLLDEN KLQFIVDTRS NKKQILEDVE KMYGFKVKSV RTMTTMKGMK KAVLAFEEPE AAHEIATRIG LM

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #21: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 13.075341 KDa
SequenceString:
MIAMVSKQPR KQRKARYAAP LHIRQKFMGA RLSEALTKEY GTRSAAVITG DTVKVMRGDF KGTEGKVQSV SLMDGTITVD GVISTKVDG TEVPRPLNPS NVMITKLEMK DGRRASSIKK

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #22: Large ribosomal subunit protein eL24

MacromoleculeName: Large ribosomal subunit protein eL24 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 7.204596 KDa
SequenceString:
MEQRKCYFCG KMLEPGTGKL YVKKDGSTYF MCSSKCMSNF ALGRLPRRTE WTEKGKIQLK KA

UniProtKB: Large ribosomal subunit protein eL24

+
Macromolecule #23: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 7.622637 KDa
SequenceString:
MAILRTSEIR TMTIEERADE LENLNNELVR ERALTSAGGA PENPGRIGEI RRTIARIKTI QHELNEI

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #24: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 17.627416 KDa
SequenceString:
MYAVVRLRGQ VNVRYTIEDT MKMLRLHKVN HCVFVPENPH YKGMVQKVKD YVAYGKIDAK TLAEVLENRG RLEGDTRLTE EYIRENTDY DSIQAFAEAV IEGKSSLKDI PKLKPVFRLH PPRKGHAGIK RTVQQGGVLG NHDENINVLL HKMR

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #25: Large ribosomal subunit protein eL30

MacromoleculeName: Large ribosomal subunit protein eL30 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 10.316188 KDa
SequenceString:
MMKMKINVDK SLIKAVKTGK VIVGANRTID AAANGSAKMV VLASNCPEDI KKKIQATDIP VLEYEGTSVE LGPVCGKPFT IAAMAILDV GESDILAATA

UniProtKB: Large ribosomal subunit protein eL30

+
Macromolecule #26: Large ribosomal subunit protein eL31

MacromoleculeName: Large ribosomal subunit protein eL31 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 10.331096 KDa
SequenceString:
MADDMVKEQI YTIPLREVRK VPAWKRANRA VIEVRGFLVR HMKTESVQVK LDKSINEHLW EKGCEKPPLS IRVRAVKFAD GEVQAELAQ

UniProtKB: Large ribosomal subunit protein eL31

+
Macromolecule #27: Large ribosomal subunit protein eL32

MacromoleculeName: Large ribosomal subunit protein eL32 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 17.880393 KDa
SequenceString:
MIMMAEEFNE VEGTNEVEDI NEVEGTSVST LDMDPESRRL FNVRKVQKGK KPQFKRTCSH KFKRLDDNWR RPRGSQGKQR RKYVSKGAL VQVGYGSPAA VKGLHPSGYS DVLISSIAEL ELVDPSYEAI RIAGTIGAQK KALILAKAEE AGIKVLNSGR S E

UniProtKB: Large ribosomal subunit protein eL32

+
Macromolecule #28: Large ribosomal subunit protein eL43

MacromoleculeName: Large ribosomal subunit protein eL43 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 10.557483 KDa
SequenceString:
MAKKFTKKGR ISRSAGRFGP RYGRKDRKLV ADLEERMRAP HVCTKCARPT VERIGTGIWK CSKCGHTFAG GTYIPYTSVG QTLLRTMKN IAEAK

UniProtKB: Large ribosomal subunit protein eL43

+
Macromolecule #29: Large ribosomal subunit protein eL37

MacromoleculeName: Large ribosomal subunit protein eL37 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 6.456628 KDa
SequenceString:
MSKGTSSMGK RQKRTHAKCR RCGSVSFNVH TKQCTSCGFG KTSRMRTYKW QAKCKY

UniProtKB: Large ribosomal subunit protein eL37

+
Macromolecule #30: Large ribosomal subunit protein eL39

MacromoleculeName: Large ribosomal subunit protein eL39 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 6.257516 KDa
SequenceString:
MSHNMKGQKK RLAKAHKQNT RVPVWVIVKT NRKVVSHPRR RHWRRRSLDV K

UniProtKB: Large ribosomal subunit protein eL39

+
Macromolecule #31: Large ribosomal subunit protein eL40

MacromoleculeName: Large ribosomal subunit protein eL40 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 5.964202 KDa
SequenceString:
MTKMARFPEA EERLLNKKIC MKCNARNAIR ATRCRKCGYG TLRVKSKESK GA

UniProtKB: Large ribosomal subunit protein eL40

+
Macromolecule #32: Large ribosomal subunit protein eL42

MacromoleculeName: Large ribosomal subunit protein eL42 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Molecular weightTheoretical: 10.872954 KDa
SequenceString:
MKIPKRFRTY CPFCKTHNEV VVERVKKGQA SSMTHIARQK KRQEGIGNSG KFSKVPGGDK PTKRIWLRYR CTVCKKAHQR PCFRAKKFE FKE

UniProtKB: Large ribosomal subunit protein eL42

+
Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 43 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #34: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 34 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris acetate
60.0 mMAmmonium chlorideNH4Cl
7.5 mMMagnessium acetateMg(CH3COO)2
6.0 mMbeta-mercaptoethanol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6skf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 61932
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.2)
FSC plot (resolution estimation)

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