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- PDB-8a98: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT -

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Basic information

Entry
Database: PDB / ID: 8a98
TitleCRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT
Components
  • (40S ribosomal protein ...) x 15
  • (60S ribosomal protein ...) x 10
  • (Putative 40S ribosomal protein ...) x 15
  • (Putative 60S ...) x 21
  • (Putative ribosomal protein ...) x 7
  • (Ribosomal protein ...) x 2
  • 5.8S_rRNA_chain_7
  • 5S_rRNA_chain_8
  • E-site_tRNA_chain_S4
  • 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
  • Small ribosomal subunit protein RACK1
  • eL13_chain_I
KeywordsRIBOSOME / CRYO-EM / LEISHMANIA MAJOR / 80S RIBOSOME snoRNA MUTANT
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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / 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 / rRNA processing / kinase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA 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 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / : / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S3, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily / Ribosomal protein S19e / Ribosomal L27e protein family / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein L30e, conserved site / Ribosomal protein S7e / Ribosomal protein L39e, conserved site / Ribosomal protein S7e / Ribosomal protein L39e signature. / 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 / Ribosomal S17 / 60S ribosomal protein L19 / 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 / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L37ae / Ribosomal L37ae protein family
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S7 / Putative ribosomal protein L1a / Putative 60S ribosomal protein L13 ...: / : / : / 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 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL5 / 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 / 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: 2.46 Å
AuthorsRajan, K.S. / Yonath, A. / Bashan, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation Israel
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
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order
Revision 1.2May 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 1.3May 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
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
SW: Putative 40S ribosomal protein S15
SZ: 40S ribosomal protein S24
SY: Putative 40S ribosomal protein S21
SX: 40S ribosomal protein S19-like protein
SV: Putative 40S ribosomal protein S17
SU: Putative 40S ribosomal protein S11
ST: Putative 40S ribosomal protein S13
SS: Putative ribosomal protein S29
SR: Putative 40S ribosomal protein S18
SB: 40S ribosomal protein SA
SC: Putative 40S ribosomal protein S3
SD: Putative 40S ribosomal protein S9
SE: 40S ribosomal protein S4
SK: 40S ribosomal protein S8
S4: E-site_tRNA_chain_S4
Sg: Small ribosomal subunit protein RACK1
Sa: 40S ribosomal protein S25
Sc: Putative 40S ribosomal protein S27-1
Se: 40S ribosomal protein S30
S1: SSU_rRNA_chain_S1
SQ: 40S ribosomal protein S12
SP: Putative 40S ribosomal protein S23
SO: 40S ribosomal protein S14
SN: Putative 40S ribosomal protein S10
Sd: Putative 40S ribosomal protein S33
SM: Putative ribosomal protein S20
SL: Putative 40S ribosomal protein S16
SJ: Putative 40S ribosomal protein S15A
SI: 40S ribosomal protein S7
SH: 40S ribosomal protein S5
SG: 40S ribosomal protein S6
SF: 40S ribosomal protein S2
SA: 40S ribosomal protein S3a
Sb: 40S ribosomal protein S26
Sh: Putative RNA binding protein
f: 60S ribosomal protein L32
d: 60S ribosomal protein L30
c: Putative 60S ribosomal protein L7
a: Putative 60S ribosomal protein L35
b: 60S ribosomal protein L29
1: LSUa_rRNA_chain_1
2: LSUb_rRNA_chain_2
4: SR2_chain_4
7: 5.8S_rRNA_chain_7
B: Putative ribosomal protein L3
8: 5S_rRNA_chain_8
5: SR4_chain_5
A: Putative 60S ribosomal protein L2
O: Putative 60S ribosomal protein L5
G: 60S ribosomal protein L7a
H: Putative 60S ribosomal protein L13a
M: Ribosomal protein L15
I: eL13_chain_I
P: 60S ribosomal protein L18
Q: Putative 60S ribosomal protein L19
R: 60S ribosomal protein L18a
E: Putative 60S ribosomal protein L9
6: SR6_chain_6
T: Putative 60S ribosomal protein L17
S: Putative 60S ribosomal protein L21
K: Putative 40S ribosomal protein L14
D: 60S ribosomal protein L11
L: Putative 60S ribosomal protein L27A/L29
Y: 60S ribosomal protein L27
Z: Putative 60S ribosomal protein L28
F: Putative 60S ribosomal protein L6
h: Putative 60S ribosomal protein L34
g: Putative ribosomal protein l35a
J: Putative 60S ribosomal protein L23
V: Putative 60S ribosomal protein L23a
W: Putative 60S ribosomal protein L26
U: Putative 60S ribosomal protein L22
i: Putative 60S Ribosomal protein L36
p: Putative 60S ribosomal protein L44
o: 60S ribosomal protein L37a
X: Putative ribosomal protein L24
k: Putative ribosomal protein L38
l: Putative 60S ribosomal protein L39
n: 60S ribosomal protein L41
C: Putative ribosomal protein L1a
3: SR1_chain_3
e: Putative 60S ribosomal subunit protein L31
j: Ribosomal protein L37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,486,329227
Polymers3,482,64683
Non-polymers3,683144
Water41,2002287
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: 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
#3: 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
#5: 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
#6: 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)
#7: 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
#9: 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
#11: 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)
Strain: BPK282A1 / References: UniProt: Q4Q4A0
#12: 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
#18: 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)
Strain: BPK282A1 / References: UniProt: Q4Q140
#22: 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)
Strain: BPK282A1 / References: UniProt: Q4QC89
#24: 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
#25: 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
#27: 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)
Strain: BPK282A1 / References: UniProt: Q4Q9A5
#28: 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
#61: 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

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40S ribosomal protein ... , 15 types, 15 molecules SZSXSBSESKSaSeSQSOSISHSGSFSASb

#2: 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
#4: Protein 40S ribosomal protein S19-like protein


Mass: 18144.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEE8
#10: 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
#13: 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
#14: 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
#17: 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
#19: 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
#21: 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
#23: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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

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

#8: 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
#26: 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)
Strain: BPK282A1 / References: UniProt: Q4Q8G4
#45: 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
#68: 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
#76: 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
#77: 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)
Strain: BPK282A1 / References: UniProt: Q4Q8X0
#80: 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

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RNA chain , 10 types, 10 molecules S4S112478563

#15: RNA chain E-site_tRNA_chain_S4


Mass: 6106.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#20: RNA chain SSU_rRNA_chain_S1


Mass: 710459.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#41: RNA chain LSUa_rRNA_chain_1


Mass: 577004.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#42: RNA chain LSUb_rRNA_chain_2


Mass: 492524.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#43: RNA chain SR2_chain_4


Mass: 59144.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321438308
#44: RNA chain 5.8S_rRNA_chain_7


Mass: 54952.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 1207899567
#46: RNA chain 5S_rRNA_chain_8


Mass: 39451.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
#47: RNA chain SR4_chain_5


Mass: 43481.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: GenBank: 321438308
#58: 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
#81: 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

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Protein , 3 types, 3 molecules SgShI

#16: Protein Small ribosomal subunit protein RACK1 / 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
#35: 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
#53: Protein eL13_chain_I


Mass: 24805.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
References: UniProt: E9AEA8

-
60S ribosomal protein ... , 10 types, 10 molecules fdbGPRDYon

#36: 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
#37: 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 L29


Mass: 8001.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Leishmania major strain Friedlin (eukaryote)
Strain: MHOM/GT/2001/U1103 / References: UniProt: Q4Q178
#50: 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
#54: 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
#56: 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
#62: 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
#64: 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
#75: 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
#79: 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)

+
Putative 60S ... , 21 types, 21 molecules caAOHQETSLZFhJVWUiple

#38: 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 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
#48: 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)
Strain: MHOM/GT/2001/U1103 / References: UniProt: Q4FWX5
#49: 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
#51: 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
#55: 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
#57: 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
#59: 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)
Strain: MHOM/GT/2001/U1103 / References: UniProt: Q4QAX6
#60: 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
#63: 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
#65: 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
#66: 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
#67: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: 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
#74: 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
#78: 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)
Strain: BPK282A1 / References: UniProt: Q4QEQ0
#82: 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

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

#52: 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
#83: 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

-
Non-polymers , 5 types, 2431 molecules

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


Mass: 24.305 Da / Num. of mol.: 130 / Source method: obtained synthetically / Formula: Mg
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#86: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#87: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#88: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2287 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

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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 snoRNA MUTANT
Type: RIBOSOME
Details: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME snoRNA MUTANT
Entity ID: #1-#83 / Source: NATURAL
Source (natural)Organism: Leishmania major strain Friedlin (eukaryote)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
2100 mMKOAc1
310 mMMg(OAc)21
410 mMNH4OAc1
51 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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: 500 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: (1.20.1_4487:phenix.real_space_refine) / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345376 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16AZ1

6az1

16AZ11PDBexperimental model
26AZ3

6az3

16AZ32PDBexperimental model
35T2A

5t2a

15T2A3PDBexperimental model
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 271.93 Å2 / Biso mean: 50.2839 Å2 / Biso min: 0 Å2

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