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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 rRNA
  • 5.8S rRNA
  • 5S rRNA
  • A-site tRNA
  • A-tRNA
  • E-tRNA
  • P-tRNA
  • RACK1
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 signature. / Ribosomal protein L10e / Ribosomal protein L7A/L8 / 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 signature. / Ribosomal protein L10e / Ribosomal protein L7A/L8 / 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
Revision 1.3Apr 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

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Structure visualization

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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


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


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


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


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


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 FIELD
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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