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- PDB-9fxo: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SIT... -

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Basic information

Entry
Database: PDB / ID: 9fxo
TitleCRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 9
  • (Putative 40S ribosomal protein ...) x 15
  • (Putative 60S ...) x 23
  • (Putative ribosomal protein ...) x 7
  • (Ribosomal protein ...) x 3
  • (Ubiquitin-60S ribosomal protein ...) x 2
  • (tRNA) x 2
  • 5.8S_rRNA_chain_7
  • 5S_rRNA_chain_8
  • Guanine nucleotide-binding protein subunit beta-like protein
  • LSUa_rRNA_chain_1
  • LSUb_rRNA_chain_2
  • Putative RNA binding protein
  • SR1_chain_3
  • SR2_chain_4
  • SR4_chain_5
  • SR6_chain_6
  • SSU_rRNA_chain_S1
  • mRNA
KeywordsRIBOSOME / CRYO-EM / LEISHMANIA MAJOR / 80S RIBOSOME / TRNA / MRNA / snoRNA
Function / homology
Function and homology information


nuclear lumen / ciliary plasm / ciliary transition zone / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled cytosolic ribosome ...nuclear lumen / ciliary plasm / ciliary transition zone / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / kinase activity / rRNA processing / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L14, KOW motif / : / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family ...Ribosomal protein L14, KOW motif / : / : / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L10e / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein L6e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L7A/L8 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / : / Ribosomal protein L30, N-terminal / Ribosomal protein L39e, conserved site / Ribosomal L30 N-terminal domain / Ribosomal protein L39e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S3, eukaryotic/archaeal / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L36e / Ribosomal protein L14e domain / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L14 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / : / Ribosomal protein S19A/S15e
Similarity search - Domain/homology
: / PAROMOMYCIN / 1,4-DIAMINOBUTANE / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S7 ...: / PAROMOMYCIN / 1,4-DIAMINOBUTANE / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S7 / Putative ribosomal protein L1a / Putative 60S ribosomal protein L13 / 40S ribosomal protein S19-like protein / Ribosomal protein L37 / 60S ribosomal protein L30 / Putative 60S ribosomal protein L5 / Putative 60S ribosomal subunit protein L31 / Putative 60S ribosomal protein L27A/L29 / Putative 60S ribosomal protein L23 / Putative 60S ribosomal protein L10 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL5 / Ubiquitin-ribosomal protein eL40 fusion protein / Putative 60S ribosomal protein L2 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL22 / Putative 40S ribosomal protein S27-1 / 60S ribosomal protein L29 / 40S ribosomal protein S24 / Putative ribosomal protein L24 / Putative 40S ribosomal protein S10 / Putative 40S ribosomal protein S18 / Ribosomal protein L3 / Putative 60S ribosomal protein L44 / Putative 40S ribosomal protein S13 / 40S ribosomal protein S3 / Putative 60S ribosomal protein L6 / Putative ribosomal protein L27 / 60S ribosomal protein L18a / Putative RNA binding protein / Ribosomal protein L15 / 40S ribosomal protein S30 / Antigen LACK / Putative 40S ribosomal protein S17 / Putative ribosomal protein S29 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S14 / 40S ribosomal protein S26 / Putative 60S ribosomal protein L35 / Large ribosomal subunit protein eL38 / Putative 40S ribosomal protein S33 / Ribosomal protein S16 / Putative 60S ribosomal protein L7 / 40S ribosomal protein S25 / Putative 60S ribosomal protein L26 / Putative 60S ribosomal protein L17 / Putative 40S ribosomal protein L14 / Putative 40S ribosomal protein S15 / 60S ribosomal protein L37a / 60S ribosomal protein L32 / Putative 40S ribosomal protein S23 / Putative 60S ribosomal protein L9 / Putative 60S Ribosomal protein L36 / Small ribosomal subunit protein uS5 / Putative 60S ribosomal protein L34 / Putative 60S ribosomal protein L39 / Putative 60S ribosomal protein L21 / Putative 60S ribosomal protein L13a / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S4 / 40S ribosomal protein S12 / Large ribosomal subunit protein eL18 / Putative 40S ribosomal protein S15A / Putative 60S ribosomal protein L28 / Putative 40S ribosomal protein S21 / Putative ribosomal protein l35a / Small ribosomal subunit protein uS4 / 60S ribosomal protein L7a / Putative 60S ribosomal protein L23a / Putative 60S ribosomal protein L19 / 40S ribosomal protein S5A / Small ribosomal subunit protein eS6
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsRajan, K.S. / Yonath, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2026
Title: A small nucleolar RNA dictates the structure and function of translating ribosomes in Leishmania.
Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale ...Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale Pescher / Tom Beneke / Masato Taoka / Christopher L Holley / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli /
Abstract: The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We ...The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We find two 2'-O-methylated positions that are differentially modified during the parasite's two life stages. The deposition of these modifications is guided by snoRNAs. When we perform cytosine base-editing of the snoRNA responsible for guiding one of the two stage-regulated modifications, Am479, we fail to detect ribosomes lacking this modification, suggesting that it is essential. To better understand the role of the snoRNA and its guided modification, we determine the cryo-EM structures of ribosomes from cells overexpressing the guiding snoRNA and compare them to ribosomes from the parental strain. We do not find structural changes around Am479 or in the small subunit rRNA, but observe a difference in H68 of the large subunit rRNA due to a second base-pairing interaction, suggesting a potential chaperone activity for the snoRNA. Based on these results, translatome and tRNA analysis, we propose a mechanism whereby changes in ribosome structure affect the release of specific tRNAs, which correlate with changes in translation of only a subset of mRNAs.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L1: LSUa_rRNA_chain_1
L2: LSUb_rRNA_chain_2
L3: SR1_chain_3
L4: SR2_chain_4
L5: SR4_chain_5
L6: SR6_chain_6
L7: 5.8S_rRNA_chain_7
L8: 5S_rRNA_chain_8
LA: Putative 60S ribosomal protein L2
LB: Putative ribosomal protein L3
LC: Putative ribosomal protein L1a
LD: 60S ribosomal protein L11
LE: Putative 60S ribosomal protein L9
LF: Putative 60S ribosomal protein L6
LG: 60S ribosomal protein L7a
LH: Putative 60S ribosomal protein L13a
LI: Putative 60S ribosomal protein L13
LJ: Putative 60S ribosomal protein L23
LK: Putative 40S ribosomal protein L14
LL: Putative 60S ribosomal protein L27A/L29
LM: Ribosomal protein L15
LN: Putative 60S ribosomal protein L10
LO: Putative 60S ribosomal protein L5
LP: 60S ribosomal protein L18
LQ: Putative 60S ribosomal protein L19
LR: 60S ribosomal protein L18a
LS: Putative 60S ribosomal protein L21
LT: Putative 60S ribosomal protein L17
LU: Putative 60S ribosomal protein L22
LV: Putative 60S ribosomal protein L23a
LW: Putative 60S ribosomal protein L26
LX: Putative ribosomal protein L24
LY: 60S ribosomal protein L27
LZ: Putative 60S ribosomal protein L28
La: Putative 60S ribosomal protein L35
Lb: 60S ribosomal protein L29
Lc: Putative 60S ribosomal protein L7
Ld: 60S ribosomal protein L30
Le: Putative 60S ribosomal subunit protein L31
Lf: 60S ribosomal protein L32
Lg: Putative ribosomal protein l35a
Lh: Putative 60S ribosomal protein L34
Li: Putative 60S Ribosomal protein L36
Lj: Ribosomal protein L37
Lk: Putative ribosomal protein L38
Ll: Putative 60S ribosomal protein L39
Lm: Ubiquitin-60S ribosomal protein L40
Ln: Ribosomal protein L41
Lo: 60S ribosomal protein L37a
Lp: Putative 60S ribosomal protein L44
S1: SSU_rRNA_chain_S1
S2: tRNA
S3: tRNA
S4: tRNA
SA: 40S ribosomal protein S3a
SB: 40S ribosomal protein SA
SC: Putative 40S ribosomal protein S3
SD: Putative 40S ribosomal protein S9
SE: 40S ribosomal protein S4
SF: 40S ribosomal protein S2
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S5
SI: 40S ribosomal protein S7
SJ: Putative 40S ribosomal protein S15A
SK: 40S ribosomal protein S8
SL: Putative 40S ribosomal protein S16
SM: Putative ribosomal protein S20
SN: Putative 40S ribosomal protein S10
SO: 40S ribosomal protein S14
SP: Putative 40S ribosomal protein S23
SQ: 40S ribosomal protein S12
SR: Putative 40S ribosomal protein S18
SS: Putative ribosomal protein S29
ST: Putative 40S ribosomal protein S13
SU: Putative 40S ribosomal protein S11
SV: Putative 40S ribosomal protein S17
SW: Putative 40S ribosomal protein S15
SX: 40S ribosomal protein S19-like protein
SY: Putative 40S ribosomal protein S21
SZ: 40S ribosomal protein S24
Sa: 40S ribosomal protein S25
Sb: 40S ribosomal protein S26
Sc: Putative 40S ribosomal protein S27-1
Sd: Putative 40S ribosomal protein S33
Se: 40S ribosomal protein S30
Sf: Ubiquitin-60S ribosomal protein L40
Sg: Guanine nucleotide-binding protein subunit beta-like protein
Sh: Putative RNA binding protein
S5: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,633,513624
Polymers3,612,21589
Non-polymers21,299535
Water49,0732724
1


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

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Components

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RNA chain , 12 types, 13 molecules L1L2L3L4L5L6L7L8S1S2S4S3S5

#1: RNA chain LSUa_rRNA_chain_1


Mass: 577129.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#2: RNA chain LSUb_rRNA_chain_2


Mass: 492571.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#3: RNA chain SR1_chain_3


Mass: 69146.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321438308
#4: RNA chain SR2_chain_4


Mass: 59466.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#5: RNA chain SR4_chain_5


Mass: 43503.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#6: RNA chain SR6_chain_6


Mass: 23336.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321438308
#7: RNA chain 5.8S_rRNA_chain_7


Mass: 54989.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#8: RNA chain 5S_rRNA_chain_8


Mass: 39756.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#51: RNA chain SSU_rRNA_chain_S1


Mass: 710765.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#52: RNA chain tRNA


Mass: 24599.748 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#53: RNA chain tRNA


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#88: RNA chain mRNA


Mass: 4085.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)

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Putative 60S ... , 23 types, 23 molecules LALELFLHLILJLLLNLOLQLSLTLULVLWLZLaLcLeLhLiLlLp

#9: Protein Putative 60S ribosomal protein L2


Mass: 28331.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4FWX5
#13: Protein Putative 60S ribosomal protein L9


Mass: 21594.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QC91
#14: Protein Putative 60S ribosomal protein L6


Mass: 21126.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q4D3
#16: Protein Putative 60S ribosomal protein L13a


Mass: 25509.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QFG2
#17: Protein Putative 60S ribosomal protein L13


Mass: 24848.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEA8
#18: Protein Putative 60S ribosomal protein L23


Mass: 14982.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AFK3
#20: Protein Putative 60S ribosomal protein L27A/L29


Mass: 16135.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AFK0
#22: Protein Putative 60S ribosomal protein L10


Mass: 24607.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: O97213
#23: Protein Putative 60S ribosomal protein L5


Mass: 34058.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AF09
#25: Protein Putative 60S ribosomal protein L19


Mass: 28896.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QJ37
#27: Protein Putative 60S ribosomal protein L21


Mass: 18068.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QEX4
#28: Protein Putative 60S ribosomal protein L17


Mass: 19124.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QAX6
#29: Protein Putative 60S ribosomal protein L22


Mass: 15030.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q0X2
#30: Protein Putative 60S ribosomal protein L23a


Mass: 16372.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QJ20
#31: Protein Putative 60S ribosomal protein L26


Mass: 16217.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QAC5
#34: Protein Putative 60S ribosomal protein L28


Mass: 16314.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QGW7
#35: Protein Putative 60S ribosomal protein L35


Mass: 15262.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q8V7
#37: Protein Putative 60S ribosomal protein L7


Mass: 28900.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q9H4
#39: Protein Putative 60S ribosomal subunit protein L31


Mass: 21316.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AFF2
#42: Protein Putative 60S ribosomal protein L34


Mass: 19335.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QDP9
#43: Protein Putative 60S Ribosomal protein L36


Mass: 11975.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QCE1
#46: Protein Putative 60S ribosomal protein L39


Mass: 6504.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QEQ0
#50: Protein Putative 60S ribosomal protein L44


Mass: 12302.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q3L3

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Putative ribosomal protein ... , 7 types, 7 molecules LBLCLXLgLkSMSS

#10: Protein Putative ribosomal protein L3


Mass: 47593.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q2Q6
#11: Protein Putative ribosomal protein L1a


Mass: 41096.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9ADW5
#32: Protein Putative ribosomal protein L24


Mass: 14608.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q1W6
#41: Protein Putative ribosomal protein l35a


Mass: 16492.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QHL3
#45: Protein Putative ribosomal protein L38


Mass: 9479.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q8X0
#66: Protein Putative ribosomal protein S20


Mass: 13031.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q8G4
#72: Protein Putative ribosomal protein S29


Mass: 6696.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q817

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60S ribosomal protein ... , 9 types, 9 molecules LDLGLPLRLYLbLdLfLo

#12: Protein 60S ribosomal protein L11


Mass: 21694.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: P48157
#15: Protein 60S ribosomal protein L7a


Mass: 29824.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QIP1
#24: Protein 60S ribosomal protein L18


Mass: 22071.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QG98
#26: Protein 60S ribosomal protein L18a


Mass: 20852.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q5J4
#33: Protein 60S ribosomal protein L27


Mass: 15469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q504
#36: Protein 60S ribosomal protein L29


Mass: 8001.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q178
#38: Protein 60S ribosomal protein L30


Mass: 11370.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEK1
#40: Protein 60S ribosomal protein L32


Mass: 15458.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QC11
#49: Protein 60S ribosomal protein L37a / Putative 60S ribosomal protein L37a


Mass: 10337.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QC01

+
Putative 40S ribosomal protein ... , 15 types, 15 molecules LKSCSDSJSLSNSPSRSTSUSVSWSYScSd

#19: Protein Putative 40S ribosomal protein L14


Mass: 19948.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QBJ1
#56: Protein Putative 40S ribosomal protein S3


Mass: 24511.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q4A0
#57: Protein Putative 40S ribosomal protein S9


Mass: 22188.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QIM3
#63: Protein Putative 40S ribosomal protein S15A


Mass: 14719.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QGW3
#65: Protein Putative 40S ribosomal protein S16 / Ribosomal protein S16


Mass: 16718.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q9A5
#67: Protein Putative 40S ribosomal protein S10


Mass: 18681.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q1X7
#69: Protein Putative 40S ribosomal protein S23


Mass: 15969.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QC89
#71: Protein Putative 40S ribosomal protein S18 / Ribosomal protein S18


Mass: 17433.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q1Y3
#73: Protein Putative 40S ribosomal protein S13


Mass: 17482.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q3M1
#74: Protein Putative 40S ribosomal protein S11


Mass: 20023.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#75: Protein Putative 40S ribosomal protein S17


Mass: 16551.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q806
#76: Protein Putative 40S ribosomal protein S15


Mass: 17472.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QBV0
#78: Protein Putative 40S ribosomal protein S21


Mass: 17035.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QH01
#82: Protein Putative 40S ribosomal protein S27-1


Mass: 9819.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q140
#83: Protein Putative 40S ribosomal protein S33


Mass: 9763.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q931

+
Ribosomal protein ... , 3 types, 3 molecules LMLjLn

#21: Protein Ribosomal protein L15


Mass: 24497.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q6S3
#44: Protein Ribosomal protein L37


Mass: 9862.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEH2
#48: Protein/peptide Ribosomal protein L41


Mass: 4390.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)

+
Ubiquitin-60S ribosomal protein ... , 2 types, 2 molecules LmSf

#47: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14711.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: P69201
#85: Protein Ubiquitin-60S ribosomal protein L40


Mass: 17062.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QFK7

+
40S ribosomal protein ... , 15 types, 15 molecules SASBSESFSGSHSISKSOSQSXSZSaSbSe

#54: Protein 40S ribosomal protein S3a / LmS3a-related protein / LmS3arp


Mass: 30062.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4FX73
#55: Protein 40S ribosomal protein SA


Mass: 27536.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q0Q0
#58: Protein 40S ribosomal protein S4


Mass: 30742.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QG31
#59: Protein 40S ribosomal protein S2


Mass: 28791.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QDL5
#60: Protein 40S ribosomal protein S6


Mass: 28370.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q9NE83
#61: Protein 40S ribosomal protein S5 / 40S ribosomal protein S5A / 40S ribosomal protein S5B


Mass: 21336.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q868B1
#62: Protein 40S ribosomal protein S7


Mass: 23765.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AC32
#64: Protein 40S ribosomal protein S8


Mass: 24984.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: P25204
#68: Protein 40S ribosomal protein S14


Mass: 15623.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q8H1
#70: Protein 40S ribosomal protein S12


Mass: 15627.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4QG97
#77: Protein 40S ribosomal protein S19-like protein


Mass: 18158.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEE8
#79: Protein 40S ribosomal protein S24


Mass: 15808.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q1D2
#80: Protein 40S ribosomal protein S25


Mass: 13071.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q9X4
#81: Protein 40S ribosomal protein S26


Mass: 12794.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q8L6
#84: Protein 40S ribosomal protein S30


Mass: 7394.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q7P0

+
Protein , 2 types, 2 molecules SgSh

#86: Protein Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34441.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q7Y7
#87: Protein Putative RNA binding protein


Mass: 25229.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: Q4Q5K7

+
Non-polymers , 8 types, 3259 molecules

#89: Chemical...
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C7H19N3
#90: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 372 / Source method: obtained synthetically / Formula: Mg
#91: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Na
#92: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: K
#93: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H12N2
#94: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#95: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#96: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2724 / Source method: isolated from a natural source / Formula: H2O

+
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT
Type: RIBOSOME / Entity ID: #3-#4, #6-#51, #54-#87 / Source: NATURAL
Source (natural)Organism: Leishmania major strain Friedlin (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 0.92 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150124 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 23.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002231406
ELECTRON MICROSCOPYf_angle_d0.4762339901
ELECTRON MICROSCOPYf_chiral_restr0.029942349
ELECTRON MICROSCOPYf_plane_restr0.003521835
ELECTRON MICROSCOPYf_dihedral_angle_d15.403780622

+
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