[English] 日本語
Yorodumi
- PDB-6skg: Cryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 dele... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6skg
TitleCryo-EM Structure of T. kodakarensis 70S ribosome in TkNat10 deleted strain
Components
  • (30S ribosomal protein ...) x 24
  • (50S ribosomal protein ...) x 32
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • LSU ribosomal protein L41E
  • Nucleic acid-binding protein, containing C2H2 zinc-finger
  • Predicted exosome subunit, UPF0023 family
  • Predicted zinc-ribbon RNA-binding protein involved in translation
  • Ribosomal protein eL35ARibosome
  • Unknown ribosomal protein
KeywordsRIBOSOME / T. kodakarensis / ac4C deletion / cryo-EM
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / mature ribosome assembly / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / small ribosomal subunit rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / mature ribosome assembly / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / ribosomal large subunit assembly / cytosolic large ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / negative regulation of translation / tRNA binding / ribosome / rRNA binding / nucleic acid binding / structural constituent of ribosome / translation / mRNA binding / RNA binding / zinc ion binding / cytosol
Ribosomal protein S13, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein L4 / Ribosomal protein L14P, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S17, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain ...Ribosomal protein S13, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein L4 / Ribosomal protein L14P, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S17, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S6e, archaeal / Ribosomal protein L3, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L15e, archaeal / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L7Ae, archaea / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein S4/S9 / Ribosomal protein S4, archaeal / Ribosomal protein L5 domain superfamily / Ribosomal protein L5, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein S12, archaea / Ribosomal protein L10e, conserved site / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosome maturation protein SBDS, conserved site / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L21e, conserved site / Ribosome maturation protein SBDS, N-terminal / Ribosomal protein L22/L17, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosome maturation protein SBDS, C-terminal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L2, domain 3 / Ribosomal protein L32e superfamily / 50S ribosomal protein L30e-like / 30S ribosomal protein S3Ae / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / EF-G domain III/V-like / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Zinc finger C2H2 superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein L22/L17 superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein S11 superfamily / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L10e, archaea / Ribosomal protein L39e domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein S15P / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S27e, zinc-binding domain superfamily
30S ribosomal protein S9 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 50S ribosomal protein L14e / Predicted exosome subunit, UPF0023 family / 50S ribosomal protein L40e / 30S ribosomal protein S2 / 30S ribosomal protein S24e / 50S ribosomal protein L37e ...30S ribosomal protein S9 / 30S ribosomal protein S11 / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 50S ribosomal protein L14e / Predicted exosome subunit, UPF0023 family / 50S ribosomal protein L40e / 30S ribosomal protein S2 / 30S ribosomal protein S24e / 50S ribosomal protein L37e / 50S ribosomal protein L21e / 50S ribosomal protein L13 / 50S ribosomal protein L18e / 30S ribosomal protein S8 / 50S ribosomal protein L34e / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 30S ribosomal protein S4e / 50S ribosomal protein L5 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L39e / 50S ribosomal protein L6 / 50S ribosomal protein L32e / 50S ribosomal protein L19e / 50S ribosomal protein L18 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 50S ribosomal protein L15e / 30S ribosomal protein S15 / 50S ribosomal protein L31e / 30S ribosomal protein S7 / 30S ribosomal protein S17e / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 30S ribosomal protein S3 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L4 / 50S ribosomal protein L10e / 50S ribosomal protein L3 / 30S ribosomal protein S6e / 50S ribosomal protein L37Ae / 30S ribosomal protein S12 / 50S ribosomal protein L18Ae / 50S ribosomal protein L30e / 30S ribosomal protein S27e / 50S ribosomal protein L44e / LSU ribosomal protein L41E / Predicted zinc-ribbon RNA-binding protein involved in translation / Nucleic acid-binding protein, containing C2H2 zinc-finger / 30S ribosomal protein S10 / 30S ribosomal protein S8e / 30S ribosomal protein S3Ae / 30S ribosomal protein S19e / 50S ribosomal protein L7Ae / 30S ribosomal protein S28e / 50S ribosomal protein L24e / gb:57158259:
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 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.
Validation Report
SummaryFull reportAbout validation report
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10224
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Aa: 16S ribosomal RNA
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 ribosomal RNA
BB: 5S ribosomal RNA
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
Bf: Ribosomal protein eL35A
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
Bm: 30S ribosomal protein S17e
Bn: 30S ribosomal protein S24e
Bo: Nucleic acid-binding protein, containing C2H2 zinc-finger
Bp: Predicted exosome subunit, UPF0023 family
Bq: Unknown ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,497,10483
Polymers2,496,18869
Non-polymers91614
Water64,0613556
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
RNA chain , 3 types, 3 molecules AaBABB

#1: RNA chain 16S ribosomal RNA / /


Mass: 487394.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#27: RNA chain 23S ribosomal RNA / /


Mass: 987981.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#28: RNA chain 5S ribosomal RNA / /


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

+
30S ribosomal protein ... , 24 types, 26 molecules AbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtBmAuAvAwBnAxAy

#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 / Ribosome / Ribosomal protein S1e / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


Mass: 8036.431 Da / Num. of mol.: 2 / 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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


Mass: 11458.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIY8
#24: Protein 30S ribosomal protein S27e / Ribosome / Ribosome


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 / Ribosome / Ribosome


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

+
Protein , 3 types, 3 molecules AzBfBp

#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
#56: Protein Ribosomal protein eL35A / Ribosome / Ribosome


Mass: 11064.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)
#64: Protein Predicted exosome subunit, UPF0023 family


Mass: 26873.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JIV0

+
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 / Ribosome / Ribosomal protein L8e / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / 50S ribosomal protein L20e / 50S ribosomal protein LX / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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 / Ribosome / Ribosome


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


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


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


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


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


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

+
Protein/peptide , 3 types, 3 molecules BkBoBq

#61: 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
#63: Protein/peptide Nucleic acid-binding protein, containing C2H2 zinc-finger


Mass: 5485.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JFH3
#65: Protein/peptide Unknown ribosomal protein


Mass: 2434.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea)

+
Non-polymers , 2 types, 3570 molecules

#66: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#67: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3556 / Source method: isolated from a natural source / Formula: H2O

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 70S ribosome from Thermococcus kodakarensisRibosome / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Buffer solutionpH: 7.5
SpecimenConc.: 0.4 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

-
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 FIELDBright-field microscopy / 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)

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116585 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more