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- PDB-6zj3: Cryo-EM structure of the highly atypical cytoplasmic ribosome of ... -

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Entry
Database: PDB / ID: 6zj3
TitleCryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis
Components
  • (60S ribosomal protein ...) x 2
  • (LSU rRNA chain ...) x 13
  • (Ribosomal protein ...) x 75
  • 18S rRNA18S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • A-site tRNA
  • A-tRNA
  • E-tRNA
  • P-tRNA
  • RACK1Receptor for activated C kinase 1
KeywordsRIBOSOME / Single particle cryo-EM RNA modifications
Function / homology
Function and homology information


cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L7A/L8 / Ribosomal protein L10e signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein L10e/L16 ...: / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L7A/L8 / Ribosomal protein L10e signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L10 / 60S ribosomal protein L7a
Similarity search - Component
Biological speciesEuglena gracilis (euglena)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMatzov, D. / Halfon, H. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Gray, M.W. / Yonath, A.E. / Shalev-Benami, M.
CitationJournal: Nucleic Acids Res / Year: 2020
Title: Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis.
Authors: Donna Matzov / Masato Taoka / Yuko Nobe / Yoshio Yamauchi / Yehuda Halfon / Nofar Asis / Ella Zimermann / Haim Rozenberg / Anat Bashan / Shashi Bhushan / Toshiaki Isobe / Michael W Gray / ...Authors: Donna Matzov / Masato Taoka / Yuko Nobe / Yoshio Yamauchi / Yehuda Halfon / Nofar Asis / Ella Zimermann / Haim Rozenberg / Anat Bashan / Shashi Bhushan / Toshiaki Isobe / Michael W Gray / Ada Yonath / Moran Shalev-Benami /
Abstract: Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from ...Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes.
History
DepositionJun 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
S1: 18S rRNA
S2: A-tRNA
S3: P-tRNA
S4: E-tRNA
S5: A-site tRNA
SA: Ribosomal protein eS1
SB: Ribosomal protein uS2
SC: Ribosomal protein uS3
SD: Ribosomal protein uS4
SE: Ribosomal protein eS4
SF: Ribosomal protein uS5
SG: Ribosomal protein eS6
SH: Ribosomal protein uS7
SI: Ribosomal protein eS7
SJ: Ribosomal protein uS8
SK: Ribosomal protein eS8
SL: Ribosomal protein uS9
SM: Ribosomal protein uS10
SN: Ribosomal protein eS10
SO: Ribosomal protein uS11
SP: Ribosomal protein uS12
SQ: Ribosomal protein eS12
SR: Ribosomal protein uS13
SS: Ribosomal protein uS14
ST: Ribosomal protein uS15
SU: Ribosomal protein uS17
SV: Ribosomal protein eS17
SW: Ribosomal protein uS19
SX: Ribosomal protein eS19
SY: Ribosomal protein eS21
SZ: Ribosomal protein eS24
Sa: Ribosomal protein eS25
Sb: Ribosomal protein eS26
Sc: Ribosomal protein eS27
Sd: Ribosomal protein eS28
Se: Ribosomal protein eS30
Sf: Ribosomal protein eS31
Sg: Ribosomal protein eSEug1
Sh: RACK1
LA: 5.8S rRNA
LB: LSU rRNA chain 1
LC: LSU rRNA chain 2
LD: LSU rRNA chain 3
LE: LSU rRNA chain 4
LF: LSU rRNA chain 5
LG: LSU rRNA chain 6
LH: LSU rRNA chain 7
LI: LSU rRNA chain 8
LJ: LSU rRNA chain 9
LK: LSU rRNA chain 10
LL: LSU rRNA chain 11
LM: LSU rRNA chain 12
LN: LSU rRNA chain 13
LO: 5S rRNA
LP: Ribosomal protein uL2
LQ: Ribosomal protein uL3
LR: Ribosomal protein uL4
LS: Ribosomal protein uL5
LT: Ribosomal protein uL6
LU: Ribosomal protein eL6
LV: 60S ribosomal protein L7a
LW: Ribosomal protein uL13
LX: Ribosomal protein eL13
LY: Ribosomal protein uL14
LZ: Ribosomal protein eL14
La: Ribosomal protein uL15
Lb: Ribosomal protein eL15
Lc: 60S ribosomal protein L10
Ld: Ribosomal protein uL18
Le: Ribosomal protein eL18
Lf: Ribosomal protein eL19
Lg: Ribosomal protein eL20
Lh: Ribosomal protein eL21
Li: Ribosomal protein uL22
Lj: Ribosomal protein eL22
Lk: Ribosomal protein uL23
Ll: Ribosomal protein uL24
Lm: Ribosomal protein eL24
Ln: Ribosomal protein eL27
Lo: Ribosomal protein eLEgr1
Lp: Ribosomal protein uL29
Lq: Ribosomal protein eL29
Lr: Ribosomal protein uL30
Ls: Ribosomal protein eL30
Lt: Ribosomal protein eL31
Lu: Ribosomal protein eL32
Lv: Ribosomal protein eL33
Lw: Ribosomal protein eL34
Lx: Ribosomal protein eL36
Ly: Ribosomal protein eL37
Lz: Ribosomal protein eL38
L1: Ribosomal protein eL39
L2: Ribosomal protein eL40
L3: Ribosomal protein eL41
L5: Ribosomal protein eL42
L4: Ribosomal protein eL43
L6: Ribosomal protein eLEgr2
L7: Ribosomal protein eLEgr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,672,469103
Polymers3,672,14298
Non-polymers3275
Water21,5101194
1


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

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Components

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RNA chain , 7 types, 7 molecules S1S2S3S4S5LALO

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 747444.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#2: RNA chain A-tRNA


Mass: 24599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#3: RNA chain P-tRNA


Mass: 24422.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#4: RNA chain E-tRNA


Mass: 24509.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#5: RNA chain A-site tRNA


Mass: 3756.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#40: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 52665.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#54: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38652.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Ribosomal protein ... , 75 types, 75 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd...

#6: Protein Ribosomal protein eS1 /


Mass: 28518.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#7: Protein Ribosomal protein uS2 /


Mass: 29244.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#8: Protein Ribosomal protein uS3 /


Mass: 24771.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#9: Protein Ribosomal protein uS4 /


Mass: 22460.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#10: Protein Ribosomal protein eS4 /


Mass: 31032.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#11: Protein Ribosomal protein uS5 /


Mass: 27936.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#12: Protein Ribosomal protein eS6 /


Mass: 31994.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#13: Protein Ribosomal protein uS7 /


Mass: 21473.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#14: Protein Ribosomal protein eS7 /


Mass: 22812.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#15: Protein Ribosomal protein uS8 /


Mass: 14943.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#16: Protein Ribosomal protein eS8 /


Mass: 35391.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#17: Protein Ribosomal protein uS9 /


Mass: 17233.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#18: Protein Ribosomal protein uS10 /


Mass: 13344.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#19: Protein Ribosomal protein eS10 /


Mass: 17060.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#20: Protein Ribosomal protein uS11 /


Mass: 16397.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#21: Protein Ribosomal protein uS12 /


Mass: 15929.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#22: Protein Ribosomal protein eS12 /


Mass: 15109.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#23: Protein Ribosomal protein uS13 /


Mass: 17632.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#24: Protein Ribosomal protein uS14 /


Mass: 6527.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#25: Protein Ribosomal protein uS15 /


Mass: 17121.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#26: Protein Ribosomal protein uS17 /


Mass: 19277.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#27: Protein Ribosomal protein eS17 /


Mass: 16399.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#28: Protein Ribosomal protein uS19 /


Mass: 17230.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#29: Protein Ribosomal protein eS19 /


Mass: 16477.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#30: Protein Ribosomal protein eS21 /


Mass: 10532.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#31: Protein Ribosomal protein eS24 /


Mass: 16123.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#32: Protein Ribosomal protein eS25 /


Mass: 13203.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#33: Protein Ribosomal protein eS26 /


Mass: 13415.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#34: Protein Ribosomal protein eS27 /


Mass: 9564.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#35: Protein Ribosomal protein eS28 /


Mass: 8510.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#36: Protein Ribosomal protein eS30 /


Mass: 7194.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#37: Protein Ribosomal protein eS31 /


Mass: 17859.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#38: Protein Ribosomal protein eSEug1 /


Mass: 32759.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#55: Protein Ribosomal protein uL2 /


Mass: 28784.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#56: Protein Ribosomal protein uL3 /


Mass: 46348.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#57: Protein Ribosomal protein uL4 /


Mass: 41993.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#58: Protein Ribosomal protein uL5 /


Mass: 21938.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#59: Protein Ribosomal protein uL6 /


Mass: 22030.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#60: Protein Ribosomal protein eL6 /


Mass: 22615.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#62: Protein Ribosomal protein uL13 /


Mass: 24602.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#63: Protein Ribosomal protein eL13 /


Mass: 25964.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#64: Protein Ribosomal protein uL14 /


Mass: 14991.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#65: Protein Ribosomal protein eL14 /


Mass: 25592.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#66: Protein Ribosomal protein uL15 /


Mass: 17320.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#67: Protein Ribosomal protein eL15 /


Mass: 24447.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#69: Protein Ribosomal protein uL18 /


Mass: 29531.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#70: Protein Ribosomal protein eL18 /


Mass: 21935.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#71: Protein Ribosomal protein eL19 /


Mass: 29130.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#72: Protein Ribosomal protein eL20 /


Mass: 21398.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#73: Protein Ribosomal protein eL21 /


Mass: 18279.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#74: Protein Ribosomal protein uL22 /


Mass: 18831.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#75: Protein Ribosomal protein eL22 /


Mass: 18961.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#76: Protein Ribosomal protein uL23 /


Mass: 18592.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#77: Protein Ribosomal protein uL24 /


Mass: 16812.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#78: Protein Ribosomal protein eL24 /


Mass: 17910.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#79: Protein Ribosomal protein eL27 /


Mass: 15562.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#80: Protein Ribosomal protein eLEgr1 /


Mass: 7961.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#81: Protein Ribosomal protein uL29 /


Mass: 14662.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#82: Protein Ribosomal protein eL29 /


Mass: 13747.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#83: Protein Ribosomal protein uL30 /


Mass: 28755.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#84: Protein Ribosomal protein eL30 /


Mass: 12053.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#85: Protein Ribosomal protein eL31 /


Mass: 17630.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#86: Protein Ribosomal protein eL32 /


Mass: 16413.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#87: Protein Ribosomal protein eL33 /


Mass: 13155.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#88: Protein Ribosomal protein eL34 /


Mass: 14908.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#89: Protein Ribosomal protein eL36 /


Mass: 12423.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#90: Protein Ribosomal protein eL37 /


Mass: 13528.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#91: Protein Ribosomal protein eL38 /


Mass: 9478.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#92: Protein Ribosomal protein eL39 /


Mass: 6499.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#93: Protein Ribosomal protein eL40 /


Mass: 14220.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#94: Protein/peptide Ribosomal protein eL41 /


Mass: 4502.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#95: Protein Ribosomal protein eL42 /


Mass: 10559.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#96: Protein Ribosomal protein eL43 /


Mass: 12340.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#97: Protein Ribosomal protein eLEgr2 /


Mass: 8128.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#98: Protein Ribosomal protein eLEgr3 /


Mass: 7499.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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Protein , 1 types, 1 molecules Sh

#39: Protein RACK1 / Receptor for activated C kinase 1


Mass: 34755.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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LSU rRNA chain ... , 13 types, 13 molecules LBLCLDLELFLGLHLILJLKLLLMLN

#41: RNA chain LSU rRNA chain 1


Mass: 42961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#42: RNA chain LSU rRNA chain 2


Mass: 113512.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#43: RNA chain LSU rRNA chain 3


Mass: 37346.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#44: RNA chain LSU rRNA chain 4


Mass: 225354.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#45: RNA chain LSU rRNA chain 5


Mass: 170807.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#46: RNA chain LSU rRNA chain 6


Mass: 75508.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#47: RNA chain LSU rRNA chain 7


Mass: 240660.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#48: RNA chain LSU rRNA chain 8


Mass: 199055.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#49: RNA chain LSU rRNA chain 9


Mass: 52952.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#50: RNA chain LSU rRNA chain 10


Mass: 20618.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#51: RNA chain LSU rRNA chain 11


Mass: 30874.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#52: RNA chain LSU rRNA chain 12


Mass: 18673.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)
#53: RNA chain LSU rRNA chain 13


Mass: 27779.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena)

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60S ribosomal protein ... , 2 types, 2 molecules LVLc

#61: Protein 60S ribosomal protein L7a /


Mass: 32999.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q4VH13
#68: Protein 60S ribosomal protein L10 /


Mass: 24695.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q39724

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Non-polymers , 2 types, 1199 molecules

#99: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#100: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1194 / 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: Euglena gracilis 80S ribosome / Type: RIBOSOME / Entity ID: #1-#98 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Euglena gracilis (euglena)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176308 / Symmetry type: POINT

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