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- PDB-7pzy: Structure of the vacant Candida albicans 80S ribosome -

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Open data

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Basic information

Entry

Database: PDB / ID: 7pzy

Title

Structure of the vacant Candida albicans 80S ribosome

Components

(40S ribosomal protein ...) x 14
(60S ribosomal protein ...) x 10
(Ribosomal 40S subunit protein ...) x 17
(Ribosomal 60S subunit protein ...) x 27
(Ribosomal protein ...) x 3
18S ribosomal RNA
25S ribosomal RNA
5.8S ribosomal RNA
5S ribosomal RNA
Guanine nucleotide-binding protein subunit beta-like protein
HABP4_PAI-RBP1 domain-containing protein
Mixture of endogenous E-tRNAs
Rpl40bp
Ubiquitin-ribosomal 40S subunit protein S31 fusion protein

Keywords

RIBOSOME /

Candida albicans /

cryo-EM

Function / homology

Function and homology information

filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / negative regulation of cell wall integrity MAPK cascade / positive regulation of conjugation with cellular fusion / filamentous growth of a population of unicellular organisms in response to biotic stimulus / yeast-form cell wall / filamentous growth of a population of unicellular organisms in response to starvation / GCN2-mediated signaling / regulation of cytoplasmic translation / fungal biofilm matrix ...filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / negative regulation of cell wall integrity MAPK cascade / positive regulation of conjugation with cellular fusion / filamentous growth of a population of unicellular organisms in response to biotic stimulus / yeast-form cell wall / filamentous growth of a population of unicellular organisms in response to starvation / GCN2-mediated signaling / regulation of cytoplasmic translation / fungal biofilm matrix / hyphal cell wall / invasive growth in response to glucose limitation / triplex DNA binding / ribosome hibernation / negative regulation of p38MAPK cascade /

translation elongation factor binding / : / regulation of translational initiation in response to stress / filamentous growth / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / 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 / translational elongation / telomeric DNA binding / mRNA destabilization / 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) / protein-RNA complex assembly /

TOR signaling / G-protein alpha-subunit binding /

ribosomal small 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) / translation regulator activity / positive regulation of autophagy / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / cellular response to starvation /

telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA /

ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome /

protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing /

protein tag activity /

ribosomal small subunit biogenesis /

ribosomal small subunit assembly / small ribosomal subunit rRNA binding /

extracellular vesicle /

ribosome biogenesis /

ribosome binding /

5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation /

rRNA binding /

cell adhesion /

ribosome / protein ubiquitination / structural constituent of ribosome /

ribonucleoprotein complex /

translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway /

mRNA binding /

ubiquitin protein ligase binding /

nucleolus / negative regulation of apoptotic process /

cell surface /

RNA binding / zinc ion binding / extracellular region /

membrane /

metal ion binding /

nucleus /

cytosol /

cytoplasm
Similarity search - Function

RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family /

Ribosomal protein L41 /

: /

Ribosomal protein S21e, conserved site /

Ribosomal protein S26e ...RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family /

Ribosomal protein L41 /

: /

Ribosomal protein S21e, conserved site /

Ribosomal protein S26e /

Ribosomal protein S26e superfamily /

Ribosomal protein S26e /

Ribosomal protein L29e /

Ribosomal protein S26e signature. /

Ribosomal protein S2, eukaryotic / Ribosomal L29e protein family /

Ribosomal protein S21e /

Ribosomal protein S21e superfamily /

Ribosomal protein S21e /

: /

Ribosomal protein S8e subdomain, eukaryotes /

Ribosomal protein S21e signature. /

Ribosomal protein S12e signature. /

Ribosomal protein S2, eukaryotic/archaeal /

Ribosomal protein S12e /

Ribosomal protein S19e / Ribosomal_S19e /

Ribosomal protein S5, eukaryotic/archaeal /

Ribosomal protein S8e, conserved site /

: /

Ribosomal protein L24e, conserved site /

Ribosomal protein S4e, N-terminal, conserved site /

40S ribosomal protein S4, C-terminal domain / Small (40S) ribosomal subunit Asc1/RACK1 /

Ribosomal protein S19e /

Ribosomal protein L22e /

Ribosomal protein L22e superfamily /

Ribosomal protein L23/L25, N-terminal / Ribosomal L22e protein family /

40S Ribosomal protein S10 /

40S ribosomal protein S4 C-terminus /

Ribosomal protein S4e, N-terminal /

Ribosomal protein L30e, conserved site /

Ribosomal protein L34e, conserved site /

Ribosomal protein S23, eukaryotic/archaeal / S27a-like superfamily /

Ribosomal protein L23, N-terminal domain / Plectin/S10, N-terminal /

Ribosomal protein S10, eukaryotic/archaeal /

Ribosomal protein L13e, conserved site /

Ribosomal protein L13e signature. / Plectin/S10 domain /

Ribosomal protein S8e /

Ribosomal protein S4, KOW domain /

Ribosomal protein S4e /

Ribosomal protein S4e, central region /

Ribosomal protein S4e, central domain superfamily /

Ribosomal protein L38e /

Ribosomal protein L38e superfamily / Ribosomal L38e protein family /

Ribosomal Protein L6, KOW domain /

Ribosomal protein L30/YlxQ /

Ribosomal protein S25 / S25 ribosomal protein / RS4NT (NUC023) domain / : /

Ribosomal protein L13e /

Ribosomal protein S17e, conserved site /

Ribosomal protein S17e signature. /

Ribosomal protein S27a /

Ribosomal protein L14e domain /

60S ribosomal protein L6E /

Ribosomal protein S30 /

Ribosomal protein L34Ae /

40S ribosomal protein S29/30S ribosomal protein S14 type Z /

Ribosomal protein L27e, conserved site /

Ribosomal protein L27e signature. /

Ribosomal protein L44e signature. / Ribosomal family S4e /

Ribosomal protein S7e signature. /

Ribosomal protein L10e, conserved site /

Ribosomal protein L10e signature. /

Ribosomal protein L32e, conserved site /

Ribosomal protein S3, eukaryotic/archaeal /

Ribosomal protein L10e /

Ribosomal protein L19, eukaryotic /

Ribosomal protein L7A/L8 /

Ribosomal protein L34e /

60S ribosomal protein L4, C-terminal domain /

Ribosomal protein L7, eukaryotic /

Ribosomal protein L6e /

Ribosomal protein L14 /

Ribosomal protein L30, N-terminal /

Ribosomal protein S3Ae, conserved site /

Ribosomal protein S3Ae signature. /

Ribosomal protein L14, KOW motif
Similarity search - Domain/homology

1,4-DIAMINOBUTANE /

SPERMIDINE /

: /

RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS21 ...

1,4-DIAMINOBUTANE /

SPERMIDINE /

: /

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 / Ribosome-associated protein STM1 / Large ribosomal subunit protein eL40 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL22 / 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 /

60S ribosomal protein L41 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein RACK1 / 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 species

Candida albicans SC5314 (yeast)

Method

ELECTRON MICROSCOPY /

single particle reconstruction /

cryo EM / Resolution: 2.32 Å

Authors

Zgadzay, Y. / Kolosova, O. / Stetsenko, A. / Jenner, L. / Guskov, A. / Yusupova, G. / Yusupov, M.

Funding support

France, 5items

Organization	Grant number	Country
Russian Science Foundation	20-65-47031	France
Russian Science Foundation	20-64-47041	France
Foundation for Medical Research (France)	FDT202106012811	France
Foundation for Medical Research (France)	DEQ20181039600	France
Foundation for Medical Research (France)	DBF20160635745	France

Citation

Journal: Sci Adv / Year: 2022
Title: E-site drug specificity of the human pathogen ribosome.
Authors: Yury Zgadzay / Olga Kolosova / Artem Stetsenko / Cheng Wu / David Bruchlen / Konstantin Usachev / Shamil Validov / Lasse Jenner / Andrey Rogachev / Gulnara Yusupova / Matthew S Sachs / ...
Abstract: is a widespread commensal fungus with substantial pathogenic potential and steadily increasing resistance to current antifungal drugs. It is known to be resistant to cycloheximide (CHX) that binds ...

History

Deposition	Oct 13, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 18, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	7pzy.cif.gz	4.4 MB	Display	PDBx/mmCIF format
PDB format	pdb7pzy.ent.gz		Display	PDB format
PDBx/mmJSON format	7pzy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pz/7pzy ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pzy	HTTPS FTP

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Related structure data

Related structure data	13737MC 13741C 13744C 13749C 13750C 7q08C 7q0fC 7q0pC 7q0rC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (78) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #10 - Oct 2000 Ribosome similarity (79) #157 - Jan 2013 Transfer-Messenger RNA similarity (3) #161 - May 2013 Ricin similarity (238) #260 - Aug 2021 Ribonuclease P similarity (7) #253 - Jan 2021 Expressome similarity (3) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (104) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (3) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (3) #65 - May 2005 Self-splicing RNA similarity (2) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (2) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #60 - Dec 2004 Ubiquitin similarity (4) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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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: 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

0: 60S ribosomal protein L20

2: Ribosomal 60S subunit protein L21A

5: Ribosomal 60S subunit protein L22B

6: Ribosomal 60S subunit protein L23B

7: Ribosomal 60S subunit protein L24A

8: Ribosomal 60S subunit protein L25

9: Ribosomal 60S subunit protein L26B

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: 60S ribosomal protein L41

AP: Ribosomal 60S subunit protein L42A

AQ: Ribosomal 60S subunit protein L43A

i: HABP4_PAI-RBP1 domain-containing protein

A: 18S ribosomal RNA

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

R: Ribosomal 40S subunit protein S16A

S: Ribosomal 40S subunit protein S17B

T: Ribosomal 40S subunit protein S18B

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

hetero molecules

3.16 MDa, 80 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author
Evidence: electron microscopy

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Components

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RNA chain , 5 types, 5 molecules 13410A

#1: RNA chain	25S ribosomal RNA / Mass: 1085306.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1078736431
#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 SC5314 (yeast) / References: GenBank: 1111963231
#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 SC5314 (yeast) / References: GenBank: 1817956650
#4: RNA chain	Mixture of endogenous E-tRNAs Mass: 24385.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Mixture of endogenous E-tRNAs / Source: (natural) Candida albicans SC5314 (yeast)
#47: RNA chain	18S ribosomal RNA / Mass: 575838.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / References: GenBank: 1078736431

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Ribosomal 60S subunit protein ... , 27 types, 27 molecules jlmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ

#5: Protein	Ribosomal 60S subunit protein L2A Mass: 27366.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: RPL2, orf19.2309.2, CAALFM_C111060CA / Production host: Candida albicans SC5314 (yeast) / References: UniProt: A0A1D8PF08
#7: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PFV1
#8: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AGZ7
#10: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PDL6
#12: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AEN2
#13: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AIB8
#14: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PHW1
#16: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PFL9
#18: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AB87
#19: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q59TE0
#20: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK43
#23: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PGY0
#24: Protein	Ribosomal 60S subunit protein L22B Mass: 14107.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PM41
#25: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PPT5
#26: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A6A1
#27: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PPS1
#28: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCQ5
#30: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PSC5
#32: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PM75
#33: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PHF5
#34: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PPN6
#35: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PHH4
#36: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PDZ1
#37: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK30
#40: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PG16
#44: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PEV4
#45: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PP14

-
60S ribosomal protein ... , 10 types, 10 molecules knpt0AAACAJAMAO

#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q59LS1
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCX8
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ANA1
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: O59931
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PLC9
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PFG4
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PF57
#38: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PH21
#41: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PDT4
#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 SC5314 (yeast) / References: UniProt: A0A2V1AQU0

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

#17: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A6R1
#21: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK40
#39: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PF45

-
Protein , 4 types, 4 molecules ANigh

#42: Protein	Rpl40bp Mass: 6078.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PL68
#46: Protein	HABP4_PAI-RBP1 domain-containing protein Mass: 29126.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK71
#79: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A109
#80: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: P83774

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

#48: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: O42817
#49: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: P40910
#52: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCI6
#54: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PL99
#55: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AJ93
#56: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q59T44
#60: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ADQ6
#69: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCG7
#70: Protein	40S ribosomal protein S22-A / Ribosome Mass: 14807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q96W54
#72: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A7K0
#73: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PNQ6
#74: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ALV6
#75: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PTI7
#78: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PSK2

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

#50: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A900
#51: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PSV5
#53: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AG43
#57: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PGY8
#58: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PI15
#59: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PN83
#61: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PPE0
#62: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PDT3
#63: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK22
#64: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCW6
#65: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PEY9
#66: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PQQ5
#67: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PK61
#68: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A389
#71: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PDU3
#76: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PQN0
#77: 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) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PTR4

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Non-polymers , 5 types, 1824 molecules

#81: Chemical	ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine Mass: 145.246 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₇H₁₉N₃
#82: Chemical	ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE / Putrescine Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂N₂
#83: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 443 / Source method: obtained synthetically / Formula: Mg
#84: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#85: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1361 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experimental details

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Candida albicans 80S ribosome / Type: RIBOSOME / Entity ID: #1-#80 / Source: NATURAL
Molecular weight	Value: 3.3 MDa / Experimental value: NO
Source (natural)	Organism: Candida albicans SC5314 (yeast)
Buffer solution	pH: 7.5
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: OTHER / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recording	Electron dose: 60 e/Å² / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correction	Type: NONE
3D reconstruction	Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243386 / Symmetry type: POINT

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RNA chain , 5 types, 5 molecules 13410A

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Ribosomal 60S subunit protein ... , 27 types, 27 molecules jlmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ

-
60S ribosomal protein ... , 10 types, 10 molecules knpt0AAACAJAMAO

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

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Protein , 4 types, 4 molecules ANigh

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

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

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Non-polymers , 5 types, 1824 molecules

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Details

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Experiment

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-RNA chain , 5 types, 5 molecules 13410A

+Ribosomal 60S subunit protein ... , 27 types, 27 molecules jlmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ

-60S ribosomal protein ... , 10 types, 10 molecules knpt0AAACAJAMAO

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

-Protein , 4 types, 4 molecules ANigh

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

-Ribosomal 40S subunit protein ... , 17 types, 17 molecules DEGKLMOPQRSTUVYde

-Non-polymers , 5 types, 1824 molecules

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RNA chain , 5 types, 5 molecules 13410A

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Ribosomal 60S subunit protein ... , 27 types, 27 molecules jlmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ

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60S ribosomal protein ... , 10 types, 10 molecules knpt0AAACAJAMAO

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

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Protein , 4 types, 4 molecules ANigh

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

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

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Non-polymers , 5 types, 1824 molecules

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Details

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Experimental details

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Experiment

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