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- PDB-9sum: CryoEM structure of Candida auris 80S ribosome in complex with Cy... -

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Basic information

Entry
Database: PDB / ID: 9sum
TitleCryoEM structure of Candida auris 80S ribosome in complex with Cycloheximide and Geneticin G418
Components
  • (40S ribosomal protein ...) x 21
  • (60S ribosomal protein ...) x 30
  • (Large ribosomal subunit protein ...) x 6
  • (Ribosomal protein ...) x 4
  • (Small ribosomal subunit protein ...) x 10
  • 18S rRNA
  • 25S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • P-site tRNA
  • RNA (5'-R(P*CP*GP*A)-3')
  • Rps21 ribosomal protein
KeywordsRIBOSOME / Candida auris / Cycloheximide / Geneticin G418 / cryoEM
Function / homology
Function and homology information


ADP transmembrane transporter activity / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / GCN2-mediated signaling / regulation of cytoplasmic translation / negative regulation of p38MAPK cascade / ribosome hibernation / preribosome / regulation of amino acid metabolic process ...ADP transmembrane transporter activity / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / yeast-form cell wall / GCN2-mediated signaling / regulation of cytoplasmic translation / negative regulation of p38MAPK cascade / ribosome hibernation / preribosome / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA destabilization / preribosome, large subunit precursor / signaling receptor activator activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational frameshifting / translational elongation / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / 90S preribosome / translational termination / protein-RNA complex assembly / ribosome-associated ubiquitin-dependent protein catabolic process / 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) / translation regulator activity / protein-membrane adaptor activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of autophagy / rescue of stalled cytosolic ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / cytosolic ribosome / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / ribosome biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 ...: / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L6e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Ribosomal protein S25 / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / : / Ribosomal protein 60S L18 and 50S L18e / : / : / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / 60S ribosomal protein L35 / Ribosomal protein L7A/L8 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L6e / Ribosomal protein S2, eukaryotic/archaeal / 60S ribosomal protein L6E / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L7, eukaryotic / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / : / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S3, eukaryotic/archaeal
Similarity search - Domain/homology
Chem-3HE / GENETICIN / SPERMIDINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L10 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL40 ...Chem-3HE / GENETICIN / SPERMIDINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L10 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein eS30 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS1 / 60S ribosomal protein L5 / 60S ribosomal protein L29 / Ribosomal protein L37 / 60S ribosomal protein L6 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein RACK1 / 60S ribosomal protein L7 / 60S ribosomal protein L32 / 40S ribosomal protein S25 / 40S ribosomal protein S22 / 60S ribosomal protein L8 / 60S ribosomal protein L43 / 60S ribosomal protein L2-A / Large ribosomal subunit protein eL14 domain-containing protein / 60S ribosomal protein L17-B / 40S ribosomal protein S8 / 60S ribosomal protein L4-A / Large ribosomal subunit protein uL3 / 40S ribosomal protein S4 / 40S ribosomal protein S15 / Ribosomal protein L19 / 60S ribosomal protein L31-A / 60S ribosomal protein L22 / 60S ribosomal protein L30 / 40S ribosomal protein S11-A / 40S ribosomal protein S24 / Small ribosomal subunit protein uS9 / 40S ribosomal protein S28-A / 40S ribosomal protein S10-A / 60S ribosomal protein L34-B / 60S ribosomal protein L27 / 60S ribosomal protein L9-B / 60S ribosomal protein L35 / Small ribosomal subunit protein uS3 / Ribosomal protein L15 / 40S ribosomal protein S13 / 60S ribosomal protein L23-B / 60S ribosomal protein L16-B / 40S ribosomal protein S9-A / 40S ribosomal protein S27 / 60S ribosomal protein L18-A / 40S ribosomal protein S19-A / 60S ribosomal protein L36 / Ribosomal protein L24 / Large ribosomal subunit protein uL23 / 40S ribosomal protein S6 / 60S ribosomal protein L44 / 40S ribosomal protein S21 / 60S ribosomal protein L11-A / 40S ribosomal protein S26 / Large ribosomal subunit protein eL38 / 40S ribosomal protein S17-B / 60S ribosomal protein L28 / 60S ribosomal protein L24 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L33-A / 60S ribosomal protein L13 / 40S ribosomal protein S23 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S18 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7 domain-containing protein / 40S ribosomal protein S7 / Small ribosomal subunit protein eS32
Similarity search - Component
Biological speciesCandidozyma auris (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsAtamas, A. / Stetsenko, A. / Incarnato, D. / Macia Valero, A. / Rogachev, A. / Billerbeck, S. / Guskov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2026
Title: Unveiling the Molecular Architecture of Candida auris Ribosome
Authors: Atamas, A. / Stetsenko, A. / Incarnato, D. / Macia Valero, A. / Rogachev, A. / Billerbeck, S. / Guskov, A.
History
DepositionSep 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: P-site tRNA
2: RNA (5'-R(P*CP*GP*A)-3')
A: 25S rRNA
B: 5S rRNA
C: 5.8S rRNA
CA: 18S rRNA
D: 60S ribosomal protein L2-A
E: Large ribosomal subunit protein uL3
F: 60S ribosomal protein L4-A
G: 60S ribosomal protein L5
H: 60S ribosomal protein L6
I: 60S ribosomal protein L7
J: 60S ribosomal protein L8
K: 60S ribosomal protein L9-B
L: 60S ribosomal protein L10
M: 60S ribosomal protein L11-A
N: 60S ribosomal protein L13
O: Large ribosomal subunit protein eL14 domain-containing protein
P: Ribosomal protein L15
Q: 60S ribosomal protein L16-B
R: 60S ribosomal protein L17-B
S: 60S ribosomal protein L18-A
T: Ribosomal protein L19
U: 60S ribosomal protein L20-A
V: 60S ribosomal protein L21-A
W: 60S ribosomal protein L22
X: 60S ribosomal protein L23-B
Y: 60S ribosomal protein L24
Z: Large ribosomal subunit protein uL23
ZA: 40S ribosomal protein S8
ZB: 40S ribosomal protein S9-A
ZC: 40S ribosomal protein S10-A
ZD: 40S ribosomal protein S11-A
ZE: 40S ribosomal protein S13
ZF: Small ribosomal subunit protein uS11
ZG: 40S ribosomal protein S15
ZH: Small ribosomal subunit protein uS9
ZI: 40S ribosomal protein S17-B
ZJ: 40S ribosomal protein S18
ZK: 40S ribosomal protein S19-A
ZL: Small ribosomal subunit protein uS10
ZM: 40S ribosomal protein S21
ZO: 40S ribosomal protein S22
ZP: 40S ribosomal protein S23
ZQ: 40S ribosomal protein S24
ZR: 40S ribosomal protein S25
ZS: 40S ribosomal protein S26
ZT: 40S ribosomal protein S27
ZU: 40S ribosomal protein S28-A
ZV: Small ribosomal subunit protein uS14
ZW: Small ribosomal subunit protein eS30
ZY: Small ribosomal subunit protein RACK1
a: Ribosomal protein L24
b: 60S ribosomal protein L27
c: 60S ribosomal protein L28
d: 60S ribosomal protein L29
e: 60S ribosomal protein L30
f: 60S ribosomal protein L31-A
g: 60S ribosomal protein L32
h: 60S ribosomal protein L33-A
i: 60S ribosomal protein L34-B
j: 60S ribosomal protein L35
k: 60S ribosomal protein L36
l: Ribosomal protein L37
m: Large ribosomal subunit protein eL38
n: Large ribosomal subunit protein eL39
o: Large ribosomal subunit protein eL40
p: Small ribosomal subunit protein eS32
q: 60S ribosomal protein L44
r: 60S ribosomal protein L43
s: Small ribosomal subunit protein uS2
t: Small ribosomal subunit protein eS1
u: Rps21 ribosomal protein
v: Small ribosomal subunit protein uS3
w: 40S ribosomal protein S4
x: 40S ribosomal protein uS7 (formerly S5)
y: 40S ribosomal protein S6
z: 40S ribosomal protein eS7 (formerly S7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,102,798400
Polymers3,067,10578
Non-polymers35,693322
Water179,4119959
1


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

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Components

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RNA chain , 6 types, 6 molecules 12ABCCA

#1: RNA chain P-site tRNA


Mass: 24445.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#2: RNA chain RNA (5'-R(P*CP*GP*A)-3')


Mass: 934.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#3: RNA chain 25S rRNA


Mass: 1061233.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#4: RNA chain 5S rRNA


Mass: 39392.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#5: RNA chain 5.8S rRNA


Mass: 50697.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#6: RNA chain 18S rRNA


Mass: 572453.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)

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60S ribosomal protein ... , 30 types, 30 molecules DFGHIJKLMNQRSUVWXYbcdefghijkqr

#7: Protein 60S ribosomal protein L2-A


Mass: 27418.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZK83
#9: Protein 60S ribosomal protein L4-A


Mass: 39776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZM70
#10: Protein 60S ribosomal protein L5


Mass: 34401.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZCP9
#11: Protein 60S ribosomal protein L6


Mass: 18547.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZD81
#12: Protein 60S ribosomal protein L7


Mass: 27510.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZFX1
#13: Protein 60S ribosomal protein L8


Mass: 29143.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZJ33
#14: Protein 60S ribosomal protein L9-B


Mass: 21692.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZVC9
#15: Protein 60S ribosomal protein L10


Mass: 25397.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A0L0NQG7
#16: Protein 60S ribosomal protein L11-A


Mass: 19645.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A6W9
#17: Protein 60S ribosomal protein L13


Mass: 22364.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A8F2VY16
#20: Protein 60S ribosomal protein L16-B


Mass: 22637.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A1L1
#21: Protein 60S ribosomal protein L17-B


Mass: 20998.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZLP7
#22: Protein 60S ribosomal protein L18-A


Mass: 20793.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A3M0
#24: Protein 60S ribosomal protein L20-A


Mass: 22128.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#25: Protein 60S ribosomal protein L21-A


Mass: 18343.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus)
#26: Protein 60S ribosomal protein L22


Mass: 13684.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZQD9
#27: Protein 60S ribosomal protein L23-B


Mass: 14529.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A034
#28: Protein 60S ribosomal protein L24


Mass: 18011.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A5C1DRN4
#54: Protein 60S ribosomal protein L27


Mass: 15454.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZUP3
#55: Protein 60S ribosomal protein L28


Mass: 16773.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A7N8
#56: Protein 60S ribosomal protein L29


Mass: 8971.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZCV4
#57: Protein 60S ribosomal protein L30


Mass: 11281.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZR23
#58: Protein 60S ribosomal protein L31-A


Mass: 13196.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZNZ0
#59: Protein 60S ribosomal protein L32


Mass: 17071.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZG69
#60: Protein 60S ribosomal protein L33-A


Mass: 12309.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A5Q7YIA8
#61: Protein 60S ribosomal protein L34-B


Mass: 13101.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZUB3
#62: Protein 60S ribosomal protein L35


Mass: 13817.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZW26
#63: Protein 60S ribosomal protein L36


Mass: 11180.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A421
#69: Protein 60S ribosomal protein L44


Mass: 12174.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A644
#70: Protein 60S ribosomal protein L43


Mass: 10758.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZK40

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Large ribosomal subunit protein ... , 6 types, 6 molecules EOZmno

#8: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3


Mass: 44056.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZM86
#18: Protein Large ribosomal subunit protein eL14 domain-containing protein


Mass: 14841.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZKB9
#29: Protein Large ribosomal subunit protein uL23 / 60S ribosomal protein L25


Mass: 15537.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A599
#65: Protein Large ribosomal subunit protein eL38 / 60S ribosomal protein L38


Mass: 8916.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A739
#66: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6404.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residue 50 was modelled as asparagine (N) based on the density map, which clearly supports N at this position.
Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A1D8PDT4
#67: Protein Large ribosomal subunit protein eL40 / 60S ribosomal protein L40-B


Mass: 6078.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A1D8PL68

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Ribosomal protein ... , 4 types, 4 molecules PTal

#19: Protein Ribosomal protein L15


Mass: 24249.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZYM3
#23: Protein Ribosomal protein L19


Mass: 24042.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZNX4
#53: Protein Ribosomal protein L24


Mass: 14303.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A4U4
#64: Protein Ribosomal protein L37


Mass: 9616.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZD58

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40S ribosomal protein ... , 21 types, 21 molecules ZAZBZCZDZEZGZIZJZKZMZOZPZQZRZSZTZUwxyz

#30: Protein 40S ribosomal protein S8


Mass: 23192.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZM29
#31: Protein 40S ribosomal protein S9-A


Mass: 21933.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A2S6
#32: Protein 40S ribosomal protein S10-A


Mass: 14494.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZTM6
#33: Protein 40S ribosomal protein S11-A


Mass: 17769.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZRL1
#34: Protein 40S ribosomal protein S13


Mass: 17045.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZYS2
#36: Protein 40S ribosomal protein S15


Mass: 15802.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZND6
#38: Protein 40S ribosomal protein S17-B


Mass: 15787.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A7E5
#39: Protein 40S ribosomal protein S18


Mass: 17042.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A8F3AFG8
#40: Protein 40S ribosomal protein S19-A


Mass: 16094.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A3R4
#42: Protein 40S ribosomal protein S21


Mass: 9676.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A6K7
#43: Protein 40S ribosomal protein S22


Mass: 14811.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZHF9
#44: Protein 40S ribosomal protein S23


Mass: 15987.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A8F2VYJ1
#45: Protein 40S ribosomal protein S24


Mass: 15557.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZS48
#46: Protein 40S ribosomal protein S25


Mass: 14507.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZGB6
#47: Protein 40S ribosomal protein S26


Mass: 20505.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A734
#48: Protein 40S ribosomal protein S27


Mass: 9027.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A3C7
#49: Protein 40S ribosomal protein S28-A


Mass: 7582.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZSJ0
#75: Protein 40S ribosomal protein S4


Mass: 29672.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZMW6
#76: Protein 40S ribosomal protein uS7 (formerly S5)


Mass: 24905.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0AB36W6W7
#77: Protein 40S ribosomal protein S6


Mass: 27054.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H1A5E3
#78: Protein 40S ribosomal protein eS7 (formerly S7)


Mass: 21459.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0AB36WC92

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Small ribosomal subunit protein ... , 10 types, 10 molecules ZFZHZLZVZWZYpstv

#35: Protein Small ribosomal subunit protein uS11


Mass: 14068.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A8F2W0L8
#37: Protein Small ribosomal subunit protein uS9


Mass: 15738.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZSF0
#41: Protein Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


Mass: 13130.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A5Q7YDP5
#50: Protein Small ribosomal subunit protein uS14 / 40S ribosomal protein S29A


Mass: 6615.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A1D8PTR4
#51: Protein Small ribosomal subunit protein eS30 / 40S ribosomal protein S30


Mass: 7127.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A1D8PSK2
#52: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein


Mass: 34479.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZFC0
#68: 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) Candidozyma auris (fungus) / References: UniProt: P9WER7
#71: Protein Small ribosomal subunit protein uS2


Mass: 29117.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZDC5
#72: Protein Small ribosomal subunit protein eS1


Mass: 28866.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZC96
#74: Protein Small ribosomal subunit protein uS3 / 40S ribosomal protein S3


Mass: 27181.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0A2H0ZW29

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Protein , 1 types, 1 molecules u

#73: Protein Rps21 ribosomal protein


Mass: 27151.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candidozyma auris (fungus) / References: UniProt: A0AB36VXE5

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Non-polymers , 6 types, 10281 molecules

#79: Chemical...
ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#80: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 253 / Source method: obtained synthetically / Formula: Mg
#81: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H19N3
#82: Chemical ChemComp-3HE / 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione


Mass: 281.347 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C15H23NO4
#83: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#84: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9959 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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 auris 80S ribosome / Type: RIBOSOME / Entity ID: #1-#78 / Source: NATURAL
Source (natural)Organism: Candidozyma auris (fungus)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 573853 / Symmetry type: POINT

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