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- PDB-6skf: Cryo-EM Structure of T. kodakarensis 70S ribosome -

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Basic information

Entry
Database: PDB / ID: 6skf
TitleCryo-EM Structure of T. kodakarensis 70S ribosome
Components
  • (30S ribosomal protein ...) x 24
  • (50S ribosomal protein ...) x 32
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • LSU ribosomal protein L41E
  • Predicted zinc-ribbon RNA-binding protein involved in translation
KeywordsRIBOSOME / T. kodakarensis / ac4C / cryo-EM
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 / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly ...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 / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / 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 L14e / : / Ribosomal protein L40e, archaeal / 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 L14e / : / Ribosomal protein L40e, archaeal / 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 L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / metallochaperone-like domain / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein S19A/S15e / Ribosomal protein L30e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S4e, N-terminal / 60S ribosomal protein L19 / RS4NT (NUC023) domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13, eukaryotic/archaeal
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL42 / LSU ribosomal protein L41E / Predicted zinc-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsMatzov, D. / Sas-Chen, A. / Thomas, J.M. / Santangelo, T. / Meier, J.L. / Schwartz, S. / Shalev-Benami, M.
CitationJournal: Nature / Year: 2020
Title: Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / ...Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / Yuko Nobe / Chloe A Briney / Michaella J Levy / Ryan T Fuchs / G Brett Robb / Jesse Hartmann / Sunny Sharma / Qishan Lin / Laurence Florens / Michael P Washburn / Toshiaki Isobe / Thomas J Santangelo / Moran Shalev-Benami / Jordan L Meier / Schraga Schwartz /
Abstract: N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics ...N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report acC-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of acC at single-nucleotide resolution. In human and yeast mRNAs, acC sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of acC across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. AcC is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of acC and its potential thermoadaptive role. Our studies quantitatively define the acC landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease.
History
DepositionAug 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 22, 2024Group: Atomic model / Category: atom_site

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
Aa: 16S rRNA
Ab: 30S ribosomal protein S2
Ac: 30S ribosomal protein S3
Ad: 30S ribosomal protein S3Ae
Ae: 30S ribosomal protein S4
Af: 30S ribosomal protein S4e
Ag: 30S ribosomal protein S5
Ah: 30S ribosomal protein S6e
Ai: 30S ribosomal protein S7
Aj: 30S ribosomal protein S8
Ak: 30S ribosomal protein S8e
Al: 30S ribosomal protein S9
Am: 30S ribosomal protein S10
An: 30S ribosomal protein S11
Ao: 30S ribosomal protein S12
Ap: 30S ribosomal protein S13
Aq: 30S ribosomal protein S15
Ar: 30S ribosomal protein S14 type Z
As: 30S ribosomal protein S17
At: 30S ribosomal protein S17e
Au: 30S ribosomal protein S19
Av: 30S ribosomal protein S19e
Aw: 30S ribosomal protein S24e
Ax: 30S ribosomal protein S27e
Ay: 30S ribosomal protein S28e
Az: Predicted zinc-ribbon RNA-binding protein involved in translation
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L7Ae
BI: 50S ribosomal protein L7Ae
BJ: 50S ribosomal protein L10e
BK: 50S ribosomal protein L13
BL: 50S ribosomal protein L14
BM: 50S ribosomal protein L14e
BN: 50S ribosomal protein L14e
BO: 50S ribosomal protein L15
BP: 50S ribosomal protein L15e
BQ: 50S ribosomal protein L18
BR: 50S ribosomal protein L18e
BS: 50S ribosomal protein L19e
BT: 50S ribosomal protein L18Ae
BU: 50S ribosomal protein L21e
BV: 50S ribosomal protein L22
BW: 50S ribosomal protein L23
BX: 50S ribosomal protein L24
BY: 50S ribosomal protein L24e
BZ: 50S ribosomal protein L29
Ba: 50S ribosomal protein L30
Bb: 50S ribosomal protein L30e
Bc: 50S ribosomal protein L31e
Bd: 50S ribosomal protein L32e
Be: 50S ribosomal protein L34e
Bg: 50S ribosomal protein L37Ae
Bh: 50S ribosomal protein L37e
Bi: 50S ribosomal protein L39e
Bj: 50S ribosomal protein L40e
Bk: LSU ribosomal protein L41E
Bl: 50S ribosomal protein L44e
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,434,81675
Polymers2,434,03163
Non-polymers78512
Water42,6422367
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
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: 488234.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#27: RNA chain 23S rRNA


Mass: 990337.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#28: RNA chain 5S rRNA


Mass: 40744.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: GenBank: 57158259

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30S ribosomal protein ... , 24 types, 24 molecules AbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAy

#2: Protein 30S ribosomal protein S2


Mass: 23039.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJD2
#3: Protein 30S ribosomal protein S3


Mass: 23390.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH5
#4: Protein 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 23064.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGM4
#5: Protein 30S ribosomal protein S4


Mass: 21240.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF2
#6: Protein 30S ribosomal protein S4e


Mass: 27820.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG0
#7: Protein 30S ribosomal protein S5


Mass: 26372.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG8
#8: Protein 30S ribosomal protein S6e


Mass: 13760.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDK8
#9: Protein 30S ribosomal protein S7


Mass: 24573.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE04
#10: Protein 30S ribosomal protein S8


Mass: 14602.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG3
#11: Protein 30S ribosomal protein S8e


Mass: 14548.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGF3
#12: Protein 30S ribosomal protein S9


Mass: 15358.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJE2
#13: Protein 30S ribosomal protein S10


Mass: 11716.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JFZ5
#14: Protein 30S ribosomal protein S11


Mass: 15111.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF3
#15: Protein 30S ribosomal protein S12


Mass: 16488.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE20
#16: Protein 30S ribosomal protein S13


Mass: 17025.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF1
#17: Protein 30S ribosomal protein S15


Mass: 17583.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGJ4
#18: Protein 30S ribosomal protein S14 type Z


Mass: 6634.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG2
#19: Protein 30S ribosomal protein S17


Mass: 13219.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH9
#20: Protein 30S ribosomal protein S17e


Mass: 8036.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDC7
#21: Protein 30S ribosomal protein S19


Mass: 15453.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH3
#22: Protein 30S ribosomal protein S19e


Mass: 17303.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGN5
#23: Protein 30S ribosomal protein S24e


Mass: 11458.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIY8
#24: Protein 30S ribosomal protein S27e


Mass: 7085.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE50
#25: Protein 30S ribosomal protein S28e


Mass: 7971.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGR4

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50S ribosomal protein ... , 32 types, 34 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBg...

#29: Protein 50S ribosomal protein L2


Mass: 26092.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH2
#30: Protein 50S ribosomal protein L3


Mass: 39118.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDJ0
#31: Protein 50S ribosomal protein L4


Mass: 28768.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDI0
#32: Protein 50S ribosomal protein L5


Mass: 21027.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG1
#33: Protein 50S ribosomal protein L6


Mass: 20888.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG4
#34: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13454.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGR3
#35: Protein 50S ribosomal protein L10e


Mass: 21116.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDI6
#36: Protein 50S ribosomal protein L13


Mass: 16316.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF6
#37: Protein 50S ribosomal protein L14


Mass: 15181.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF8
#38: Protein 50S ribosomal protein L14e


Mass: 8968.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJE4
#39: Protein 50S ribosomal protein L15


Mass: 16571.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJH0
#40: Protein 50S ribosomal protein L15e


Mass: 22607.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JH43
#41: Protein 50S ribosomal protein L18


Mass: 22895.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG7
#42: Protein 50S ribosomal protein L18e


Mass: 13799.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF5
#43: Protein 50S ribosomal protein L19e


Mass: 17667.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG6
#44: Protein 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 9227.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGT3
#45: Protein 50S ribosomal protein L21e


Mass: 11290.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JI51
#46: Protein 50S ribosomal protein L22


Mass: 17838.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH4
#47: Protein 50S ribosomal protein L23


Mass: 9915.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH1
#48: Protein 50S ribosomal protein L24


Mass: 14225.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF9
#49: Protein 50S ribosomal protein L24e


Mass: 8111.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGR5
#50: Protein 50S ribosomal protein L29


Mass: 7937.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDH6
#51: Protein 50S ribosomal protein L30


Mass: 17856.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG9
#52: Protein 50S ribosomal protein L30e


Mass: 10972.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE35
#53: Protein 50S ribosomal protein L31e


Mass: 10354.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGT5
#54: Protein 50S ribosomal protein L32e


Mass: 14654.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJG5
#55: Protein 50S ribosomal protein L34e


Mass: 10558.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJF7
#56: Protein 50S ribosomal protein L37Ae / Ribosomal protein L43e


Mass: 9240.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDM6
#57: Protein 50S ribosomal protein L37e


Mass: 7470.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIE1
#58: Protein 50S ribosomal protein L39e


Mass: 6262.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JGT6
#59: Protein 50S ribosomal protein L40e


Mass: 5781.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJD3
#61: Protein 50S ribosomal protein L44e


Mass: 11204.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE51

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Protein / Protein/peptide , 2 types, 2 molecules AzBk

#26: Protein Predicted zinc-ribbon RNA-binding protein involved in translation


Mass: 7001.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JFE2
#60: Protein/peptide LSU ribosomal protein L41E


Mass: 5051.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JEV0

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Non-polymers , 2 types, 2379 molecules

#62: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#63: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 70S ribosome from Thermococcus kodakarensis / Type: RIBOSOME / Entity ID: #1-#61 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Buffer solutionpH: 7.5
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 29000 X / C2 aperture diameter: 70 µm
Image recordingElectron dose: 34 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53737 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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