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- PDB-9g6j: The structure of the Candida albicans ribosome with tRNA-fMet, mR... -

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Basic information

Entry
Database: PDB / ID: 9g6j
TitleThe structure of the Candida albicans ribosome with tRNA-fMet, mRNA, and compounds (GEN and MFQ) with strong density for the P-site tRNA
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 9
  • (Ribosomal 40S subunit protein ...) x 17
  • (Ribosomal 60S subunit protein ...) x 26
  • (Ribosomal protein ...) x 3
  • 18S rRNA
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Rpl40bp
  • Small ribosomal subunit protein eS32
  • Ubiquitin-ribosomal 40S subunit protein S31 fusion protein
  • mRNA
  • tRNA-fMet
KeywordsRIBOSOME / Candida albicans / mRNA / mefloquine / geneticin G418
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / fungal biofilm matrix / GCN2-mediated signaling / regulation of cytoplasmic translation ...filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / fungal biofilm matrix / GCN2-mediated signaling / regulation of cytoplasmic translation / invasive growth in response to glucose limitation / hyphal cell wall / negative regulation of p38MAPK cascade / filamentous growth / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / nonfunctional rRNA decay / mRNA destabilization / signaling receptor activator activity / negative regulation of translational frameshifting / negative regulation of mRNA splicing, via spliceosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / regulation of amino acid metabolic process / G-protein alpha-subunit binding / ribosomal subunit export from nucleus / 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) / protein-RNA complex assembly / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / positive regulation of autophagy / rescue of stalled ribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to starvation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase C binding / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / extracellular vesicle / 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 / cell adhesion / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / cell surface / RNA binding / zinc ion binding / extracellular region / nucleus / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...: / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 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 L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / : / Plectin/S10 domain / Ribosomal protein S7e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / : / : / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S17e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S3Ae, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae signature. / 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 / 40S ribosomal protein S4, C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein S27e signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein L30e, conserved site / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal Protein L6, KOW domain
Similarity search - Domain/homology
GENETICIN / SPERMINE (FULLY PROTONATED FORM) / Mefloquine / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) ...GENETICIN / SPERMINE (FULLY PROTONATED FORM) / Mefloquine / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL22 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL8B / Small ribosomal subunit protein uS8A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Candida albicans SC5314 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å
AuthorsKolosova, O. / Zgadzay, Y. / Jenner, L.B. / Guskov, A. / Yusupov, M.
Funding support France, 3items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)FDT202204014886 France
Foundation for Medical Research (France)DBF20160635745 France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Mechanism of read-through enhancement by aminoglycosides and mefloquine.
Authors: Olga Kolosova / Yury Zgadzay / Artem Stetsenko / Anastasia P Sukhinina / Anastasia Atamas / Shamil Validov / Andrey Rogachev / Konstantin Usachev / Lasse Jenner / Sergey E Dmitriev / Gulnara ...Authors: Olga Kolosova / Yury Zgadzay / Artem Stetsenko / Anastasia P Sukhinina / Anastasia Atamas / Shamil Validov / Andrey Rogachev / Konstantin Usachev / Lasse Jenner / Sergey E Dmitriev / Gulnara Yusupova / Albert Guskov / Marat Yusupov /
Abstract: Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of ...Nonsense mutations are associated with numerous and diverse pathologies, yet effective treatment strategies remain elusive. A promising approach to combat these conditions involves the use of aminoglycosides, particularly in combination with stop-codon read-through enhancers, for developing drugs that can rescue the production of full-length proteins. Using X-ray crystallography and single-particle cryo-EM, we obtained structures of the eukaryotic ribosome in complexes with several aminoglycosides (geneticin G418, paromomycin, and hygromycin B) and the antimalarial drug mefloquine (MFQ), which has also been identified as a read-through enhancer. Our study reveals a binding site of MFQ, which holds significant promise for the development of therapies targeting premature termination codon-related genetic and oncological diseases. The results underscore the crucial role of the bridge B7b/c in mediating the effects of MFQ on subunit rotation dynamics. Through a comprehensive analysis of the interactions between the drugs and the eukaryotic ribosome, we propose a unifying hypothesis for read-through enhancement by small molecules, highlighting the role of decoding center rearrangements and intersubunit rotation dynamics.
History
DepositionJul 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 60S ribosomal protein L20
1: 25S rRNA
2: Ribosomal 60S subunit protein L21A
3: 5S rRNA
4: 5.8S rRNA
6: Ribosomal 60S subunit protein L23B
7: Ribosomal 60S subunit protein L24A
8: Ribosomal 60S subunit protein L25
9: Ribosomal 60S subunit protein L26B
A: 18S rRNA
B: 40S ribosomal protein S0
C: 40S ribosomal protein S1
D: Ribosomal 40S subunit protein S2
E: Ribosomal 40S subunit protein S3
F: 40S ribosomal protein S4
G: Ribosomal 40S subunit protein S5
H: 40S ribosomal protein S6
I: 40S ribosomal protein S7
J: 40S ribosomal protein S8
K: Ribosomal 40S subunit protein S9B
L: Ribosomal 40S subunit protein S10A
M: Ribosomal 40S subunit protein S11A
N: 40S ribosomal protein S12
O: Ribosomal 40S subunit protein S13
P: Ribosomal 40S subunit protein S14B
Q: Ribosomal 40S subunit protein S15
T: Ribosomal 40S subunit protein S18B
R: Ribosomal 40S subunit protein S16A
S: Ribosomal 40S subunit protein S17B
U: Ribosomal 40S subunit protein S19A
V: Ribosomal 40S subunit protein S20
W: 40S ribosomal protein S21
X: 40S ribosomal protein S22-A
Y: Ribosomal 40S subunit protein S23B
Z: 40S ribosomal protein S24
a: 40S ribosomal protein S25
b: 40S ribosomal protein S26
c: 40S ribosomal protein S27
d: Ribosomal 40S subunit protein S28B
e: Ribosomal 40S subunit protein S29A
f: 40S ribosomal protein S30
g: Ubiquitin-ribosomal 40S subunit protein S31 fusion protein
h: Guanine nucleotide-binding protein subunit beta-like protein
j: Ribosomal 60S subunit protein L2A
k: 60S ribosomal protein L3
l: Ribosomal 60S subunit protein L4B
m: Ribosomal 60S subunit protein L5
n: 60S ribosomal protein L6
o: Ribosomal 60S subunit protein L7A
p: 60S ribosomal protein L8
q: Ribosomal 60S subunit protein L9B
r: Ribosomal 60S subunit protein L10
s: Ribosomal 60S subunit protein L11B
t: 60S ribosomal protein L13
u: Ribosomal 60S subunit protein L14B
v: Ribosomal protein L15
w: Ribosomal 60S subunit protein L16A
x: Ribosomal 60S subunit protein L17B
y: Ribosomal 60S subunit protein L18A
z: Ribosomal protein L19
AA: 60S ribosomal protein L27
AB: Ribosomal 60S subunit protein L28
AC: 60S ribosomal protein L29
AD: Ribosomal 60S subunit protein L30
AE: Ribosomal 60S subunit protein L31B
AF: Ribosomal 60S subunit protein L32
AG: Ribosomal 60S subunit protein L33A
AH: Ribosomal 60S subunit protein L34B
AI: Ribosomal 60S subunit protein L35A
AJ: 60S ribosomal protein L36
AK: Ribosomal protein L37
AL: Ribosomal 60S subunit protein L38
AM: 60S ribosomal protein L39
AN: Rpl40bp
AO: Small ribosomal subunit protein eS32
AP: Ribosomal 60S subunit protein L42A
AQ: Ribosomal 60S subunit protein L43A
PT: tRNA-fMet
MR: mRNA
AT: tRNA-fMet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,146,794105
Polymers3,137,80680
Non-polymers8,98725
Water00
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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60S ribosomal protein ... , 9 types, 9 molecules 0knptAAACAJAM

#1: Protein 60S ribosomal protein L20


Mass: 20376.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PLC9
#45: Protein 60S ribosomal protein L3


Mass: 44040.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q59LS1
#48: Protein 60S ribosomal protein L6


Mass: 19798.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PCX8
#50: Protein 60S ribosomal protein L8


Mass: 28549.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5ANA1
#54: Protein 60S ribosomal protein L13


Mass: 23105.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: O59931
#61: Protein 60S ribosomal protein L27


Mass: 15551.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PFG4
#63: Protein 60S ribosomal protein L29


Mass: 7135.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PF57
#70: Protein 60S ribosomal protein L36


Mass: 11096.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PH21
#73: Protein 60S ribosomal protein L39


Mass: 6347.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PDT4

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RNA chain , 6 types, 7 molecules 134APTATMR

#2: RNA chain 25S rRNA


Mass: 1085306.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1078736431
#4: RNA chain 5S rRNA


Mass: 38943.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1111963231
#5: RNA chain 5.8S rRNA


Mass: 50683.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1817956650
#10: RNA chain 18S rRNA


Mass: 575838.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1078736431
#78: RNA chain tRNA-fMet


Mass: 24802.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli DH5[alpha] (bacteria) / References: GenBank: 1848851804
#79: RNA chain mRNA


Mass: 12383.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast)

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Ribosomal 60S subunit protein ... , 26 types, 26 molecules 26789jlmoqrsuwxyABADAEAFAGAHAIALAPAQ

#3: Protein Ribosomal 60S subunit protein L21A


Mass: 18049.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PGY0
#6: Protein Ribosomal 60S subunit protein L23B


Mass: 14508.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PPT5
#7: Protein Ribosomal 60S subunit protein L24A


Mass: 17430.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A6A1
#8: Protein Ribosomal 60S subunit protein L25


Mass: 15873.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PPS1
#9: Protein Ribosomal 60S subunit protein L26B


Mass: 14215.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PCQ5
#44: Protein Ribosomal 60S subunit protein L2A


Mass: 27366.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PF08
#46: Protein Ribosomal 60S subunit protein L4B


Mass: 39282.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PFV1
#47: Protein Ribosomal 60S subunit protein L5


Mass: 34557.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AGZ7
#49: Protein Ribosomal 60S subunit protein L7A


Mass: 27446.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PDL6
#51: Protein Ribosomal 60S subunit protein L9B


Mass: 21755.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AEN2
#52: Protein Ribosomal 60S subunit protein L10


Mass: 25236.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AIB8
#53: Protein Ribosomal 60S subunit protein L11B


Mass: 19859.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PHW1
#55: Protein Ribosomal 60S subunit protein L14B


Mass: 14748.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PFL9
#57: Protein Ribosomal 60S subunit protein L16A


Mass: 22685.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AB87
#58: Protein Ribosomal 60S subunit protein L17B


Mass: 21002.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q59TE0
#59: Protein Ribosomal 60S subunit protein L18A


Mass: 20817.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PK43
#62: Protein Ribosomal 60S subunit protein L28


Mass: 16703.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PSC5
#64: Protein Ribosomal 60S subunit protein L30


Mass: 11520.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PM75
#65: Protein Ribosomal 60S subunit protein L31B


Mass: 12993.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PHF5
#66: Protein Ribosomal 60S subunit protein L32


Mass: 14993.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PPN6
#67: Protein Ribosomal 60S subunit protein L33A


Mass: 12138.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PHH4
#68: Protein Ribosomal 60S subunit protein L34B


Mass: 13774.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PDZ1
#69: Protein Ribosomal 60S subunit protein L35A


Mass: 14118.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PK30
#72: Protein Ribosomal 60S subunit protein L38


Mass: 8911.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PG16
#76: Protein Ribosomal 60S subunit protein L42A


Mass: 12285.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PEV4
#77: Protein Ribosomal 60S subunit protein L43A


Mass: 10136.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PP14

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40S ribosomal protein ... , 14 types, 14 molecules BCFHIJNWXZabcf

#11: Protein 40S ribosomal protein S0


Mass: 28759.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: O42817
#12: Protein 40S ribosomal protein S1 / S3aE


Mass: 29041.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: P40910
#15: Protein 40S ribosomal protein S4


Mass: 29435.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PCI6
#17: Protein 40S ribosomal protein S6


Mass: 27146.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PL99
#18: Protein 40S ribosomal protein S7


Mass: 21285.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AJ93
#19: Protein 40S ribosomal protein S8


Mass: 22801.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q59T44
#23: Protein 40S ribosomal protein S12


Mass: 15715.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5ADQ6
#32: Protein 40S ribosomal protein S21


Mass: 9652.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PCG7
#33: Protein 40S ribosomal protein S22-A


Mass: 14807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q96W54
#35: Protein 40S ribosomal protein S24


Mass: 15546.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A7K0
#36: Protein 40S ribosomal protein S25


Mass: 11633.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PNQ6
#37: Protein 40S ribosomal protein S26


Mass: 13606.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5ALV6
#38: Protein 40S ribosomal protein S27


Mass: 8982.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PTI7
#41: Protein 40S ribosomal protein S30


Mass: 7127.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PSK2

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Ribosomal 40S subunit protein ... , 17 types, 17 molecules DEGKLMOPQTRSUVYde

#13: Protein Ribosomal 40S subunit protein S2


Mass: 26917.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A900
#14: Protein Ribosomal 40S subunit protein S3


Mass: 27313.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PSV5
#16: Protein Ribosomal 40S subunit protein S5


Mass: 25319.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5AG43
#20: Protein Ribosomal 40S subunit protein S9B


Mass: 21765.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PGY8
#21: Protein Ribosomal 40S subunit protein S10A


Mass: 13836.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PI15
#22: Protein Ribosomal 40S subunit protein S11A


Mass: 17638.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PN83
#24: Protein Ribosomal 40S subunit protein S13


Mass: 16976.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PPE0
#25: Protein Ribosomal 40S subunit protein S14B


Mass: 14052.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PDT3
#26: Protein Ribosomal 40S subunit protein S15


Mass: 15967.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PK22
#27: Protein Ribosomal 40S subunit protein S18B


Mass: 17023.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PQQ5
#28: Protein Ribosomal 40S subunit protein S16A


Mass: 15769.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PCW6
#29: Protein Ribosomal 40S subunit protein S17B


Mass: 15770.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PEY9
#30: Protein Ribosomal 40S subunit protein S19A


Mass: 16097.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PK61
#31: Protein Ribosomal 40S subunit protein S20


Mass: 13366.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A389
#34: Protein Ribosomal 40S subunit protein S23B


Mass: 16000.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PDU3
#39: Protein Ribosomal 40S subunit protein S28B


Mass: 7536.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PQN0
#40: Protein Ribosomal 40S subunit protein S29A


Mass: 6615.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PTR4

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Protein , 3 types, 3 molecules ghAN

#42: Protein Ubiquitin-ribosomal 40S subunit protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A109
#43: Protein Guanine nucleotide-binding protein subunit beta-like protein / Cytoplasmic antigenic protein 1


Mass: 34593.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: P83774
#74: Protein Rpl40bp


Mass: 6078.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PL68

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Ribosomal protein ... , 3 types, 3 molecules vzAK

#56: Protein Ribosomal protein L15


Mass: 24389.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: Q5A6R1
#60: Protein Ribosomal protein L19


Mass: 21942.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PK40
#71: Protein Ribosomal protein L37


Mass: 10102.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PF45

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Protein/peptide , 1 types, 1 molecules AO

#75: Protein/peptide Small ribosomal subunit protein eS32 / 60S ribosomal protein L41 / Large ribosomal subunit protein eL41


Mass: 3396.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: UniProt: P9WER7

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Non-polymers , 4 types, 25 molecules

#80: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM)


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#81: Chemical
ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C20H40N4O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#83: Chemical ChemComp-YMZ / (11R,12S)- Mefloquine


Mass: 378.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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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: Candida albicans ribosome in complex with initiator fMet-tRNA, mRNA, and GEN+MFQ
Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Molecular weightValue: 3.3 MDa / Experimental value: NO
Source (natural)Organism: Candida albicans SC5314 (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1200 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 29.7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19rc4_4035: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63238 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007212135
ELECTRON MICROSCOPYf_angle_d0.808311743
ELECTRON MICROSCOPYf_dihedral_angle_d15.09274789
ELECTRON MICROSCOPYf_chiral_restr0.04839219
ELECTRON MICROSCOPYf_plane_restr0.00920124

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