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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


ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, 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) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome ...ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, 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) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / 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 / rRNA processing / kinase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / 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 / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L14, KOW motif / : / 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 L14, KOW motif / : / 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 L29e / Ribosomal L29e protein family / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L19, eukaryotic / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / Ribosomal protein 60S L18 and 50S L18e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / : / 40S ribosomal protein S4 C-terminus / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S19e / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / : / Ribosomal protein S19A/S15e / Ribosomal protein L6e / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / 60S ribosomal protein L19 / Ribosomal S17 / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / 60S ribosomal protein L6E / 60S ribosomal protein L35 / Ribosomal protein L13, eukaryotic/archaeal / : / Ribosomal S24e conserved site
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 / 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 / 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 / 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: 2.25 Å
AuthorsRajan, K.S. / Yonath, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT
Authors: Rajan, K.S. / Yonath, A.
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

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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

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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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