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- PDB-8rxx: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-sit... -

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Basic information

Entry
Database: PDB / ID: 8rxx
TitleCRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : LM32Cs3H1 sKO STRAIN
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 10
  • (Putative 40S ribosomal protein ...) x 14
  • (Putative 60S ...) x 23
  • (Putative ribosomal protein ...) x 7
  • (Ribosomal protein ...) x 3
  • (Ubiquitin-60S ribosomal protein ...) x 2
  • 5.8S_rRNA_chain_7
  • 5S_rRNA_chain_8
  • A-site_tRNA_chain_S2
  • E-site_tRNA_chain_S4
  • Guanine nucleotide-binding protein subunit beta-like protein
  • LSUa_rRNA_chain_1
  • LSUb_rRNA_chain_2
  • P-site_tRNA_chain_S3
  • Putative RNA binding protein
  • SR1_chain_3
  • SR2_chain_4
  • SR4_chain_5
  • SR6_chain_6
  • SSU_rRNA_chain_S1
  • mRNA_chain_S5
KeywordsRIBOSOME / CRYO-EM / LEISHMANIA MAJOR / 80S
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) / protein-RNA complex assembly / translation regulator activity / 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) / 90S preribosome ...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) / protein-RNA complex assembly / translation regulator activity / 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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / kinase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / phosphorylation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein S7e / Ribosomal protein L30e, conserved site / Ribosomal protein S7e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / 60S ribosomal protein L19 / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature.
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 / Ubiquitin-ribosomal protein eL40 fusion protein / 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: 2.97 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
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 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
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: 60S ribosomal protein L41
Lo: 60S ribosomal protein L37a
Lp: Putative 60S ribosomal protein L44
S1: SSU_rRNA_chain_S1
S2: A-site_tRNA_chain_S2
S3: P-site_tRNA_chain_S3
S4: E-site_tRNA_chain_S4
S5: mRNA_chain_S5
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: Ribosomal protein S17 family protein
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,620,226388
Polymers3,611,57389
Non-polymers8,653299
Water17,835990
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 13 types, 13 molecules L1L2L3L4L5L6L7L8S1S2S3S4S5

#1: RNA chain LSUa_rRNA_chain_1


Mass: 577111.688 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: 492557.906 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: 43479.801 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: 54975.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 2105481105
#8: 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
#51: RNA chain SSU_rRNA_chain_S1


Mass: 710614.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#52: RNA chain A-site_tRNA_chain_S2


Mass: 24599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#53: RNA chain P-site_tRNA_chain_S3


Mass: 24786.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#54: RNA chain E-site_tRNA_chain_S4


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#55: RNA chain mRNA_chain_S5


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
#68: 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
#74: 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 ... , 10 types, 10 molecules LDLGLPLRLYLbLdLfLnLo

#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
#48: 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)
#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 ... , 14 types, 14 molecules LKSCSDSJSLSNSPSRSTSVSWSYScSd

#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
#58: 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
#59: 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
#65: 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
#67: 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
#69: 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
#71: 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
#73: 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
#75: 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
#77: 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
#78: 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
#80: 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
#84: 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
#85: 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 LMLjSU

#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
#76: Protein Ribosomal protein S17 family protein


Mass: 20023.457 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
#87: 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

#56: 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
#57: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#66: 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
#70: 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
#72: 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
#79: 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
#81: 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
#82: 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
#83: 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
#86: 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

#88: 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
#89: 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 , 5 types, 1289 molecules

#90: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: K
#91: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Na
#92: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#93: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#94: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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 WITH A/P/E-site tRNA AND mRNA / Type: RIBOSOME
Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : LM32Cs3H1 sKO STRAIN
Entity ID: #1-#50, #52-#89 / 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 FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1.273 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490938 / Symmetry type: POINT

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