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- PDB-8ogj: Structure of Candida albicans 80S ribosome in complex with mefloquine -

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Basic information

Entry
Database: PDB / ID: 8ogj
TitleStructure of Candida albicans 80S ribosome in complex with mefloquine
Components
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 37
  • (Ribosomal protein ...) x 10
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Mixture of endogenous E-tRNAs
  • Ubiquitin-40S ribosomal protein S31 fusion protein
KeywordsRIBOSOME / Candida albicans / mefloquine
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 / regulation of cytoplasmic translation / GCN2-mediated signaling / invasive growth in response to glucose limitation ...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 / regulation of cytoplasmic translation / GCN2-mediated signaling / invasive growth in response to glucose limitation / hyphal cell wall / preribosome / negative regulation of p38MAPK cascade / filamentous growth / regulation of amino acid metabolic process / 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 / translational elongation / G-protein alpha-subunit binding / 90S preribosome / ribosomal subunit export from nucleus / protein-RNA complex assembly / ribosomal small subunit export from nucleus / translation regulator activity / positive regulation of autophagy / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to starvation / 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 / modification-dependent protein catabolic process / protein tag activity / rRNA processing / extracellular vesicle / ribosome biogenesis / large ribosomal subunit / 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 / cell adhesion / 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 / extracellular region / zinc ion binding / metal ion binding / nucleus / 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 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / 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 L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / 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 S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / 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 L30e signature 1. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / 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 protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily
Similarity search - Domain/homology
SPERMINE (FULLY PROTONATED FORM) / Mefloquine / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...SPERMINE (FULLY PROTONATED FORM) / Mefloquine / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS14 / 60S ribosomal protein L42-B / Ribosomal protein S7 / 40S ribosomal protein S17-B / 40S ribosomal protein S26 / Ribosomal protein L22 / 60S ribosomal protein L7-A / 60S ribosomal protein L28 / 60S ribosomal protein L33-A / 40S ribosomal protein S27 / 40S ribosomal protein S10-A / Ribosomal protein S10 / 40S ribosomal protein S3 / 40S ribosomal protein S6 / Ribosomal protein L13 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L20 / 40S ribosomal protein S28-B / 60S ribosomal protein L8 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S12 / 40S ribosomal protein S24 / 60S ribosomal protein L9-B / 60S ribosomal protein L23-A / 60S ribosomal protein L24-A / 60S ribosomal protein L18-A / 40S ribosomal protein S19-A / 40S ribosomal protein S7 / 40S ribosomal protein S25 / 60S ribosomal protein L29 / 40S ribosomal protein S22-A / 40S ribosomal protein S8 / Ribosomal protein S23 (S12) / 40S ribosomal protein S14-A / 60S ribosomal protein L34-B / 60S ribosomal protein L21-A / 60S ribosomal protein L31-B / 60S ribosomal protein L11-B / Ribosomal protein S4 / 60S ribosomal protein L2-B / 60S ribosomal protein L14-B / Ribosomal protein L24 / 40S ribosomal protein S18-B / 40S ribosomal protein S13 / 60S ribosomal protein L4-B / 60S ribosomal protein L13 / 60S ribosomal protein L25 / Ribosomal protein L29 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein RACK1 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL3 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS21
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKolosova, O. / Zgadzay, Y. / Stetsenko, A. / Guskov, A. / Yusupov, M.
Funding support France, Russian Federation, 4items
OrganizationGrant numberCountry
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
Foundation for Medical Research (France)FDT202204014886 France
Russian Science Foundation20-65-47031 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Mechanism of read-through enhancement by aminoglycosides and mefloquine
Authors: Kolosova, O. / Zgadzay, Y. / Yusupov, M.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Apr 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
10: Mixture of endogenous E-tRNAs
j: 60S ribosomal protein L2-B
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-B
m: 60S ribosomal protein L5
n: 60S ribosomal protein L6
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8
q: 60S ribosomal protein L9-B
r: 60S ribosomal protein L10
s: 60S ribosomal protein L11-B
t: 60S ribosomal protein L13
u: 60S ribosomal protein L14-B
v: 60S ribosomal protein L15-A
w: Ribosomal protein L13
x: Ribosomal protein L22
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-B
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: Ribosomal protein L24
AA: 60S ribosomal protein L27
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-B
AF: 60S ribosomal protein L32
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-B
AI: Ribosomal protein L29
AJ: 60S ribosomal protein L36
AK: 60S ribosomal protein L37-B
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: 60S ribosomal protein L40-B
AO: 60S ribosomal protein L41
AP: 60S ribosomal protein L42-B
AQ: 60S ribosomal protein L43-A
A: 18S ribosomal RNA
B: 40S ribosomal protein S0
C: 40S ribosomal protein S1
D: Ribosomal protein S5
E: Ribosomal protein S3
F: 40S ribosomal protein S4
G: Ribosomal protein S7
H: 40S ribosomal protein S6
I: 40S ribosomal protein S7
J: 40S ribosomal protein S8
K: Ribosomal protein S4
L: 40S ribosomal protein S10-A
M: 40S ribosomal protein S11A
N: 40S ribosomal protein S12
O: 40S ribosomal protein S13
P: 40S ribosomal protein S14-A
Q: 40S ribosomal protein S15
R: 40S ribosomal protein S16
S: 40S ribosomal protein S17-B
T: 40S ribosomal protein S18-B
U: 40S ribosomal protein S19-A
V: Ribosomal protein S10
W: 40S ribosomal protein S21
X: 40S ribosomal protein S22-A
Y: Ribosomal protein S23 (S12)
Z: 40S ribosomal protein S24
a: 40S ribosomal protein S25
b: 40S ribosomal protein S26
c: 40S ribosomal protein S27
d: 40S ribosomal protein S28-B
e: 40S ribosomal protein S29A
f: 40S ribosomal protein S30
g: Ubiquitin-40S ribosomal protein S31 fusion protein
h: Guanine nucleotide-binding protein subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,126,099520
Polymers3,114,24379
Non-polymers11,855441
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 13410A

#1: RNA chain 25S ribosomal RNA


Mass: 1085278.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086444.1
#2: RNA chain 5S ribosomal RNA


Mass: 38943.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: X16634.1
#3: RNA chain 5.8S ribosomal RNA


Mass: 50683.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: OQ195134.1
#4: RNA chain Mixture of endogenous E-tRNAs


Mass: 24385.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: correct sequence GGCAGCAUAGCUCAGUUGGUUAGAGCGUAGGACUCAUAAGCCUAAGGUCACUGGUUCAAUUCCAGUUCUGCUACCA (GGCAG-gap-CUGCUACCA)
Source: (natural) Candida albicans (yeast)
#46: RNA chain 18S ribosomal RNA


Mass: 575838.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: GenBank: XR_002086442.1

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60S ribosomal protein ... , 37 types, 37 molecules jklmnopqrstuvyz025678AAABACADAEAFAGAHAJ...

#5: Protein 60S ribosomal protein L2-B


Mass: 27366.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X9
#6: Protein 60S ribosomal protein L3


Mass: 44040.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q59LS1
#7: Protein 60S ribosomal protein L4-B


Mass: 39282.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4H4
#8: Protein 60S ribosomal protein L5


Mass: 34557.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5AGZ7
#9: Protein 60S ribosomal protein L6


Mass: 19798.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P834
#10: Protein 60S ribosomal protein L7-A


Mass: 27446.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVN2
#11: Protein 60S ribosomal protein L8


Mass: 28549.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C337
#12: Protein 60S ribosomal protein L9-B


Mass: 21755.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3N3
#13: Protein 60S ribosomal protein L10


Mass: 25236.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5AIB8
#14: Protein 60S ribosomal protein L11-B


Mass: 19859.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1S5
#15: Protein 60S ribosomal protein L13


Mass: 23105.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F5V7
#16: Protein 60S ribosomal protein L14-B


Mass: 14748.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F332
#17: Protein 60S ribosomal protein L15-A


Mass: 24389.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A6R1
#20: Protein 60S ribosomal protein L18-A


Mass: 20817.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4Y1
#21: Protein 60S ribosomal protein L19-A


Mass: 21942.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK40
#22: Protein 60S ribosomal protein L20


Mass: 20376.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZJ3
#23: Protein 60S ribosomal protein L21-A


Mass: 18049.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1C8
#24: Protein 60S ribosomal protein L22-B


Mass: 14107.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM41
#25: Protein 60S ribosomal protein L23-A


Mass: 14494.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C444
#26: Protein 60S ribosomal protein L24-A


Mass: 17430.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C4U1
#27: Protein 60S ribosomal protein L25


Mass: 15873.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6A1
#29: Protein 60S ribosomal protein L27


Mass: 15551.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P843
#30: Protein 60S ribosomal protein L28


Mass: 16703.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BVY8
#31: Protein 60S ribosomal protein L29


Mass: 7135.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0G8
#32: Protein 60S ribosomal protein L30


Mass: 11520.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PM75
#33: Protein 60S ribosomal protein L31-B


Mass: 12993.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1M1
#34: Protein 60S ribosomal protein L32


Mass: 14993.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94008
#35: Protein 60S ribosomal protein L33-A


Mass: 12138.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BW57
#36: Protein 60S ribosomal protein L34-B


Mass: 13774.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F171
#38: Protein 60S ribosomal protein L36 / L39


Mass: 11096.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P47834
#39: Protein 60S ribosomal protein L37-B


Mass: 10102.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PF45
#40: Protein 60S ribosomal protein L38


Mass: 8911.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PG16
#41: Protein 60S ribosomal protein L39 / L46


Mass: 6347.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q96W55
#42: Protein 60S ribosomal protein L40-B


Mass: 6078.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PL68
#43: Protein/peptide 60S ribosomal protein L41


Mass: 3396.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: P9WER7
#44: Protein 60S ribosomal protein L42-B


Mass: 12259.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BR69
#45: Protein 60S ribosomal protein L43-A


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

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Ribosomal protein ... , 10 types, 10 molecules wx9AIDEGKVY

#18: Protein Ribosomal protein L13


Mass: 22685.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ56
#19: Protein Ribosomal protein L22


Mass: 21002.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BUG0
#28: Protein Ribosomal protein L24


Mass: 14215.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3X2
#37: Protein Ribosomal protein L29


Mass: 14118.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F6B7
#49: Protein Ribosomal protein S5


Mass: 26917.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ90
#50: Protein Ribosomal protein S3


Mass: 27313.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYS1
#52: Protein Ribosomal protein S7


Mass: 25319.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BS29
#56: Protein Ribosomal protein S4


Mass: 21765.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F1X2
#67: Protein Ribosomal protein S10


Mass: 13366.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BYJ9
#70: Protein Ribosomal protein S23 (S12)


Mass: 16000.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V0

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40S ribosomal protein ... , 25 types, 25 molecules BCFHIJLMNOPQRSTUWXZabcdef

#47: Protein 40S ribosomal protein S0


Mass: 28759.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C395
#48: Protein 40S ribosomal protein S1


Mass: 29041.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C387
#51: Protein 40S ribosomal protein S4


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


Mass: 27146.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BZ37
#54: Protein 40S ribosomal protein S7


Mass: 21285.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C655
#55: Protein 40S ribosomal protein S8


Mass: 22801.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0S0
#57: Protein 40S ribosomal protein S10-A


Mass: 13836.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWQ8
#58: Protein 40S ribosomal protein S11A


Mass: 17638.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PN83
#59: Protein 40S ribosomal protein S12


Mass: 15715.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3A1
#60: Protein 40S ribosomal protein S13


Mass: 16976.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F4G0
#61: Protein 40S ribosomal protein S14-A


Mass: 14052.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F0V4
#62: Protein 40S ribosomal protein S15


Mass: 15967.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PK22
#63: Protein 40S ribosomal protein S16


Mass: 15769.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: O94017
#64: Protein 40S ribosomal protein S17-B


Mass: 15770.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTR7
#65: Protein 40S ribosomal protein S18-B


Mass: 17023.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6F3Y8
#66: Protein 40S ribosomal protein S19-A


Mass: 16097.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C5L4
#68: Protein 40S ribosomal protein S21


Mass: 9652.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q9P844
#69: 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 (yeast) / References: UniProt: A0A8H6F0N4
#71: Protein 40S ribosomal protein S24


Mass: 15546.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C3K1
#72: Protein 40S ribosomal protein S25


Mass: 11633.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6EZQ8
#73: Protein 40S ribosomal protein S26


Mass: 13606.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BTS1
#74: Protein 40S ribosomal protein S27


Mass: 8982.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6BWE6
#75: Protein 40S ribosomal protein S28-B


Mass: 7536.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A8H6C0A5
#76: Protein 40S ribosomal protein S29A


Mass: 6615.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: A0A1D8PTR4
#77: Protein 40S ribosomal protein S30


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

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Protein , 2 types, 2 molecules gh

#78: Protein Ubiquitin-40S ribosomal protein S31 fusion protein


Mass: 22615.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast) / References: UniProt: Q5A109
#79: Protein Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein ASC1 / Absence of growth suppressor of Cyp1 protein 1 / Cytoplasmic antigenic protein 1


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

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Non-polymers , 4 types, 441 molecules

#80: Chemical ChemComp-YMZ / (11R,12S)- Mefloquine


Mass: 378.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16F6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#81: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM)


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#82: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 432 / Source method: obtained synthetically / Formula: Mg
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Candida albicans 80S ribosome in complex with mefloquine
Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Molecular weightValue: 3.3 MDa / Experimental value: YES
Source (natural)Organism: Candida albicans (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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 16000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm
Image recordingElectron dose: 47.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49801 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004210875
ELECTRON MICROSCOPYf_angle_d0.78309449
ELECTRON MICROSCOPYf_dihedral_angle_d15.39173426
ELECTRON MICROSCOPYf_chiral_restr0.04638740
ELECTRON MICROSCOPYf_plane_restr0.00720340

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