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- PDB-9o17: Cryo-EM structure of Methanosarcina acetivorans 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 9o17
TitleCryo-EM structure of Methanosarcina acetivorans 70S ribosome
Components
  • (Large ribosomal subunit protein ...) x 30
  • (Small ribosomal subunit protein ...) x 24
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Putative zinc finger domain-containing protein
KeywordsRIBOSOME / Archaea / Methanosarcina acetivorans / 70S 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / cytosol
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 L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, 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 L40e, archaeal / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 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 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 S5, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / Ribosomal protein S2, eukaryotic/archaeal / 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 S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein 60S L18 and 50S L18e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / 60S ribosomal protein L19 / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 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 S24e conserved site / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein S24e signature. / Ribosomal protein L37ae
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / DUF1610 domain-containing protein / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL32 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / DUF1610 domain-containing protein / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsGhosh, A. / Fordjour, G.N.R. / Armache, J.-P. / Ferry, J.G. / Murakami, K.S. / Bevilacqua, P.C.
Funding support United States, 3items
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
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S rRNA
AB: Small ribosomal subunit protein uS2
AC: Small ribosomal subunit protein uS3
AD: Small ribosomal subunit protein eS1
AE: Small ribosomal subunit protein uS4
AF: Small ribosomal subunit protein eS4
AG: Small ribosomal subunit protein uS5
AI: Small ribosomal subunit protein uS7
AJ: Small ribosomal subunit protein uS8
AK: Small ribosomal subunit protein eS8
AL: Small ribosomal subunit protein uS9
AN: Small ribosomal subunit protein uS11
AO: Small ribosomal subunit protein uS12
AP: Small ribosomal subunit protein uS13
AR: Small ribosomal subunit protein uS14
AQ: Small ribosomal subunit protein uS15
AS: Small ribosomal subunit protein uS17A
AU: Small ribosomal subunit protein uS19
AV: Small ribosomal subunit protein eS19
AW: Small ribosomal subunit protein eS24
AX: Small ribosomal subunit protein eS27
AY: Small ribosomal subunit protein eS28
AH: Small ribosomal subunit protein eS6
AM: Small ribosomal subunit protein uS10
AT: Small ribosomal subunit protein eS17
BA: 23S rRNA
BB: 5S rRNA
BC: Large ribosomal subunit protein uL2
BD: Large ribosomal subunit protein uL3
BE: Large ribosomal subunit protein uL4
BF: Large ribosomal subunit protein uL5
BG: Large ribosomal subunit protein uL6
BH: Large ribosomal subunit protein eL8
BI: Large ribosomal subunit protein uL16
BJ: Large ribosomal subunit protein uL13
BK: Large ribosomal subunit protein uL14
BL: Large ribosomal subunit protein uL15
BM: Large ribosomal subunit protein eL15
BN: Large ribosomal subunit protein uL18
BO: Large ribosomal subunit protein eL18
BP: Large ribosomal subunit protein eL19
BQ: Large ribosomal subunit protein eL20
BR: Large ribosomal subunit protein eL21
BS: Large ribosomal subunit protein uL22
BT: Large ribosomal subunit protein uL23
BU: Large ribosomal subunit protein uL24
BV: Large ribosomal subunit protein eL24
BW: Large ribosomal subunit protein uL29
BX: Large ribosomal subunit protein uL30
BY: Large ribosomal subunit protein eL30
BZ: Large ribosomal subunit protein eL31
Ba: Large ribosomal subunit protein eL32
Bb: Large ribosomal subunit protein eL43
Bc: Large ribosomal subunit protein eL37
Bd: Large ribosomal subunit protein eL39
Be: Large ribosomal subunit protein eL40
Bf: Large ribosomal subunit protein eL42
AZ: Putative zinc finger domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,311,797118
Polymers2,309,96958
Non-polymers1,82860
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules AABABB

#1: RNA chain 16S rRNA


Mass: 478373.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 470466243
#26: RNA chain 23S rRNA


Mass: 937667.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 19918815
#27: RNA chain 5S rRNA


Mass: 41399.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: GenBank: 19918815

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Small ribosomal subunit protein ... , 24 types, 24 molecules ABACADAEAFAGAIAJAKALANAOAPARAQASAUAVAWAXAYAHAMAT

#2: Protein Small ribosomal subunit protein uS2


Mass: 27234.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832VZ76
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 34780.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU1
#4: Protein Small ribosomal subunit protein eS1 / 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 22938.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TKI9
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 24559.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR1
#6: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 26301.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT5
#7: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 22732.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS7
#8: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 21062.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRC2
#9: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14085.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT2
#10: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 13801.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TS82
#11: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14512.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT42
#12: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13324.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR0
#13: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15540.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRC1
#14: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 20693.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRR2
#15: Protein/peptide Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 5971.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT3
#16: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 17503.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TS56
#17: Protein Small ribosomal subunit protein uS17A / 30S ribosomal protein S17 1


Mass: 12184.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT8
#18: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 15467.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU3
#19: Protein Small ribosomal subunit protein eS19


Mass: 16563.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9Q0
#20: Protein Small ribosomal subunit protein eS24 / 30S ribosomal protein S24e


Mass: 11620.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJT2
#21: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 6955.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: P61931
#22: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 8268.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL8
#23: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 14474.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL4
#24: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11380.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: P61929
#25: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 7477.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8THP2

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Large ribosomal subunit protein ... , 30 types, 30 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBf

#28: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 25738.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU4
#29: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 36949.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU7
#30: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 27516.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU6
#31: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 18398.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT4
#32: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19530.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT1
#33: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 12741.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL9
#34: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 19409.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TU90
#35: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16085.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT43
#36: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 14356.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT7
#37: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15129.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS5
#38: Protein Large ribosomal subunit protein eL15 / 50S ribosomal protein L15e


Mass: 22650.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TPX0
#39: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 19233.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS8
#40: Protein Large ribosomal subunit protein eL18 / 50S ribosomal protein L18e


Mass: 13714.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TT44
#41: Protein Large ribosomal subunit protein eL19


Mass: 17061.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9G6
#42: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 6972.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN5
#43: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11063.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQU3
#44: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 16764.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU2
#45: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 9447.194 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU5
#46: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 13075.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRT6
#47: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7204.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TQL7
#48: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7622.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRU0
#49: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 17627.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRS6
#50: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10316.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TRB9
#51: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 10331.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN3
#52: Protein Large ribosomal subunit protein eL32


Mass: 17880.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W8Z7
#53: Protein Large ribosomal subunit protein eL43


Mass: 10557.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832SMV9
#54: Protein Large ribosomal subunit protein eL37 / 50S ribosomal protein L37e


Mass: 6456.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TL48
#55: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6257.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TIN2
#56: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 5964.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: Q8TJ19
#57: Protein Large ribosomal subunit protein eL42


Mass: 10872.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832W9V9

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Protein , 1 types, 1 molecules AZ

#58: Protein Putative zinc finger domain-containing protein


Mass: 6162.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina acetivorans (archaea) / References: UniProt: A0A832S8D7

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Non-polymers , 2 types, 60 molecules

#59: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: Mg
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Methanosarcina acetivorans 70S ribosome / Type: RIBOSOME / Entity ID: #1-#58 / Source: NATURAL
Source (natural)Organism: Methanosarcina acetivorans (archaea)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris acetate1
260 mMAmmonium chlorideNH4Cl1
37.5 mMMagnessium acetateMg(CH3COO)21
46 mMbeta-mercaptoethanol1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.2particle selection
2EPUimage acquisition
4cryoSPARCv4.6.2CTF correction
7UCSF ChimeraXv1.7model fitting
8ISOLDEmodel fitting
10Cootv0.9.8.95model refinement
11PHENIXv1.20.1model refinement
12cryoSPARCv4.6.2initial Euler assignment
13cryoSPARCv4.6.2final Euler assignment
15cryoSPARCv4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91385 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043161341
ELECTRON MICROSCOPYf_angle_d0.7147239343
ELECTRON MICROSCOPYf_chiral_restr0.038830321
ELECTRON MICROSCOPYf_plane_restr0.005314205
ELECTRON MICROSCOPYf_dihedral_angle_d14.204760280

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