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- PDB-8ovj: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN -

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Basic information

Entry
Database: PDB / ID: 8ovj
TitleCRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 10
  • (Putative 40S ribosomal protein ...) x 15
  • (Putative 60S ...) x 23
  • (Putative ribosomal protein ...) x 7
  • (Ribosomal protein ...) x 2
  • 5.8S_rRNA_chain_7
  • 5S_rRNA_chain_8
  • E-site_tRNA_chain_S4
  • Guanine nucleotide-binding protein subunit beta-like protein
  • LSUa_rRNA_chain_1
  • LSUb_rRNA_chain_2
  • Putative RNA binding proteinRNA-binding protein
  • SR1_chain_3
  • SR2_chain_4
  • SR4_chain_5
  • SR6_chain_6
  • SSU_rRNA_chain_S1
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / CRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
Function / homology
Function and homology information


ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / ribosomal small subunit biogenesis / protein tag activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / large ribosomal subunit rRNA binding / small ribosomal subunit / kinase activity / cytosolic small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein L29e / Ribosomal protein S26e ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein L29e / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L29e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L10e / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal S17 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L22e protein family / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L34Ae / Ribosomal protein S3Ae / Plectin/S10, N-terminal / Ribosomal S3Ae family / Ribosomal protein S7e / Ribosomal L27e protein family / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S4, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein L34e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L37ae / RS4NT (NUC023) domain / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L44e signature. / Ribosomal protein S28e / Ribosomal protein L10e signature. / Ribosomal family S4e / Ribosomal protein L19, eukaryotic / Ribosomal protein L7A/L8
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S7 / Putative ribosomal protein L1a ...: / : / : / : / 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 / 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 / Activated protein kinase c receptor / Putative 40S ribosomal protein S17 / Putative ribosomal protein S29 / Putative ribosomal protein S20 / 40S ribosomal protein S14 / 40S ribosomal protein S26 / Putative 60S ribosomal protein L35 / Putative ribosomal protein L38 / 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 / 40S ribosomal protein S2 / Large ribosomal subunit protein eL34 / Putative 60S ribosomal protein L39 / Putative 60S ribosomal protein L21 / Putative 60S ribosomal protein L13a / 40S ribosomal protein S4 / 40S ribosomal protein S12 / Large ribosomal subunit protein eL18 / Putative 40S ribosomal protein S15A / Large ribosomal subunit protein eL28 / Putative 40S ribosomal protein S21 / Putative ribosomal protein l35a / Putative 40S ribosomal protein S9 / 60S ribosomal protein L7a / Putative 60S ribosomal protein L23a / Putative 60S ribosomal protein L19 / 40S ribosomal protein S5 / Small ribosomal subunit protein eS6
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRajan, K.S. / Yonath, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Cell Rep / Year: 2024
Title: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.
Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / ...Authors: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / Aliza Fedorenko / Tanaya Bose / Ella Zimermann / Eric Prina / Noa Aharon-Hefetz / Yitzhak Pilpel / Toshiaki Isobe / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli /
Abstract: Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the ...Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: LSUa_rRNA_chain_1
3: SR1_chain_3
4: SR2_chain_4
5: SR4_chain_5
6: SR6_chain_6
7: 5.8S_rRNA_chain_7
8: 5S_rRNA_chain_8
A: Putative 60S ribosomal protein L2
B: Putative ribosomal protein L3
C: Putative ribosomal protein L1a
D: 60S ribosomal protein L11
E: Putative 60S ribosomal protein L9
F: Putative 60S ribosomal protein L6
G: 60S ribosomal protein L7a
H: Putative 60S ribosomal protein L13a
I: Putative 60S ribosomal protein L13
J: Putative 60S ribosomal protein L23
K: Putative 40S ribosomal protein L14
L: Putative 60S ribosomal protein L27A/L29
M: Ribosomal protein L15
N: Putative 60S ribosomal protein L10
O: Putative 60S ribosomal protein L5
P: 60S ribosomal protein L18
Q: Putative 60S ribosomal protein L19
R: 60S ribosomal protein L18a
S1: SSU_rRNA_chain_S1
S4: E-site_tRNA_chain_S4
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
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
S: Putative 60S ribosomal protein L21
Sa: 40S ribosomal protein S25
Sc: Putative 40S ribosomal protein S27-1
Sb: 40S ribosomal protein S26
Sd: Putative 40S ribosomal protein S33
Se: 40S ribosomal protein S30
Sg: Guanine nucleotide-binding protein subunit beta-like protein
Sh: Putative RNA binding protein
SJ: Putative 40S ribosomal protein S15A
T: Putative 60S ribosomal protein L17
U: Putative 60S ribosomal protein L22
V: Putative 60S ribosomal protein L23a
W: Putative 60S ribosomal protein L26
X: Putative ribosomal protein L24
Y: 60S ribosomal protein L27
Z: Putative 60S ribosomal protein L28
a: Putative 60S ribosomal protein L35
b: 60S ribosomal protein L29
c: Putative 60S ribosomal protein L7
d: 60S ribosomal protein L30
e: Putative 60S ribosomal subunit protein L31
f: 60S ribosomal protein L32
g: Putative ribosomal protein l35a
h: Putative 60S ribosomal protein L34
i: Putative 60S Ribosomal protein L36
j: Ribosomal protein L37
k: Putative ribosomal protein L38
l: Putative 60S ribosomal protein L39
m: Ubiquitin-60S ribosomal protein L40
n: 60S ribosomal protein L41
o: 60S ribosomal protein L37a
p: Putative 60S ribosomal protein L44
2: LSUb_rRNA_chain_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,532,343452
Polymers3,522,60485
Non-polymers9,739367
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 10 types, 10 molecules 1345678S1S42

#1: RNA chain LSUa_rRNA_chain_1


Mass: 577046.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321438308
#2: 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
#3: RNA chain SR2_chain_4


Mass: 59160.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#4: RNA chain SR4_chain_5


Mass: 43479.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#5: 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
#6: 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)
References: GenBank: 1207899567
#7: RNA chain 5S_rRNA_chain_8


Mass: 39450.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321399712
#26: RNA chain SSU_rRNA_chain_S1


Mass: 710628.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#27: RNA chain E-site_tRNA_chain_S4


Mass: 6451.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#85: RNA chain LSUb_rRNA_chain_2


Mass: 492500.781 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 AEFHIJLNOQSTUVWZacehilp

#8: 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
#12: 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
#13: 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
#15: Protein Putative 60S ribosomal protein L13a / Ribosome


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
#16: 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
#17: 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
#19: Protein Putative 60S ribosomal protein L27A/L29 / Ribosome


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
#21: 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
#22: 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
#24: 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
#53: 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
#62: 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
#63: 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
#64: Protein Putative 60S ribosomal protein L23a / Ribosome


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
#65: 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
#68: 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
#69: 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
#71: 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
#73: 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
#76: 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
#77: 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
#80: 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
#84: 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 BCSMSSXgk

#9: 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
#10: Protein Putative ribosomal protein L1a / Ribosome


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
#39: 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
#45: 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
#66: 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
#75: Protein Putative ribosomal protein l35a / Ribosome


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
#79: 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

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60S ribosomal protein ... , 10 types, 10 molecules DGPRYbdfno

#11: 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
#14: 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
#23: 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
#25: 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
#67: 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
#70: 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
#72: 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
#74: 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
#82: Protein/peptide 60S 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)
#83: 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

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Putative 40S ribosomal protein ... , 15 types, 15 molecules KSCSDSLSNSPSRSTSUSVSWSYScSdSJ

#18: 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
#30: 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
#31: 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
#38: 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
#40: 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
#42: 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
#44: 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
#46: 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
#47: 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)
#48: 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
#49: 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
#51: 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
#55: Protein Putative 40S ribosomal protein S27-1 / Ribosome


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
#57: 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
#61: Protein Putative 40S ribosomal protein S15A / Ribosome


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

-
Ribosomal protein ... , 2 types, 2 molecules Mj

#20: 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
#78: 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

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

#28: 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
#29: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#41: 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
#43: 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
#50: Protein 40S ribosomal protein S19-like protein / Ribosome


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
#52: 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
#54: 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
#56: 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
#58: 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 , 3 types, 3 molecules SgShm

#59: 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
#60: Protein Putative RNA binding protein / 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
#81: 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

-
Non-polymers , 5 types, 416 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 302 / Source method: obtained synthetically / Formula: Mg
#87: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: K
#88: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#89: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 80S RIBOSOME FROM LEISHMANIA MAJOREukaryotic ribosome / Type: RIBOSOME / Entity ID: #1-#85 / 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
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 FIELDBright-field microscopy / Nominal defocus max: 1300 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 0.83 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212912 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003215441
ELECTRON MICROSCOPYf_angle_d0.578316901
ELECTRON MICROSCOPYf_dihedral_angle_d15.69875062
ELECTRON MICROSCOPYf_chiral_restr0.03739712
ELECTRON MICROSCOPYf_plane_restr0.00420545

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