[English] 日本語
Yorodumi
- PDB-7q08: Structure of Candida albicans 80S ribosome in complex with cycloh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q08
TitleStructure of Candida albicans 80S ribosome in complex with cycloheximide
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 9
  • (Ribosomal 40S subunit protein ...) x 17
  • (Ribosomal 60S subunit protein ...) x 28
  • (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
  • Rpl40bp
  • Ubiquitin-ribosomal 40S subunit protein S31 fusion protein
KeywordsRIBOSOME / Candida albicans / cycloheximide / drug design
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 integrity MAPK cascade / positive regulation of conjugation with cellular fusion / 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 / yeast-form cell wall / 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 integrity MAPK cascade / positive regulation of conjugation with cellular fusion / 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 / yeast-form cell wall / GCN2-mediated signaling / regulation of cytoplasmic translation / fungal biofilm matrix / hyphal cell wall / invasive growth in response to glucose limitation / triplex DNA binding / negative regulation of p38MAPK cascade / ribosome hibernation / 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 / telomeric DNA binding / mRNA destabilization / negative regulation of mRNA splicing, via spliceosome / translational elongation / G-protein alpha-subunit binding / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / positive regulation of autophagy / translation regulator activity / translation repressor activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / telomere maintenance / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to starvation / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / extracellular vesicle / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / cell adhesion / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / cell surface / RNA binding / zinc ion binding / extracellular region / membrane / nucleus / metal ion binding / 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 S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. ...RNA binding protein HABP4/SERBP1 / Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / : / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein L44e / Ribosomal protein L24e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L44 / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S27e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein L30e signature 2.
Similarity search - Domain/homology
Chem-3HE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS4 ...Chem-3HE / 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 / 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 speciesCandida albicans SC5314 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsZgadzay, Y. / Kolosova, O. / Stetsenko, A. / Jenner, L. / Guskov, A. / Yusupova, G. / Yusupov, M.
Funding support France, 5items
OrganizationGrant numberCountry
Russian Science Foundation20-65-47031 France
Russian Science Foundation20-64-47041 France
Foundation for Medical Research (France)FDT202106012811 France
Foundation for Medical Research (France)DEQ20181039600 France
Foundation for Medical Research (France)DBF20160635745 France
CitationJournal: 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 / ...Authors: Yury Zgadzay / Olga Kolosova / Artem Stetsenko / Cheng Wu / David Bruchlen / Konstantin Usachev / Shamil Validov / Lasse Jenner / Andrey Rogachev / Gulnara Yusupova / Matthew S Sachs / Albert Guskov / Marat Yusupov /
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 ... 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 to the E-transfer RNA binding site of the ribosome. Because of lack of structural information, it is neither possible to understand the nature of the resistance nor to develop novel inhibitors. To overcome this issue, we determined the structure of the vacant 80 ribosome at 2.3 angstroms and its complexes with bound inhibitors at resolutions better than 2.9 angstroms using cryo-electron microscopy. Our structures reveal how a change in a conserved amino acid in ribosomal protein eL42 explains CHX resistance in and forms a basis for further antifungal drug development.
History
DepositionOct 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
j: Ribosomal 60S subunit protein L2A
k: Ribosomal 60S subunit 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 eL41
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


Theoretical massNumber of molelcules
Total (without water)3,120,00189
Polymers3,119,05179
Non-polymers95010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 4 types, 4 molecules 134A

#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)
#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 SC5314 (yeast) / References: GenBank: 1078736431

+
Ribosomal 60S subunit protein ... , 28 types, 28 molecules jklmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ

#4: Protein Ribosomal 60S subunit protein L2A


Mass: 27366.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PF08
#5: Protein Ribosomal 60S subunit 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
#6: 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
#7: 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
#9: 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
#11: 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
#12: 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
#13: 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
#15: 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
#17: 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
#18: 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
#19: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#29: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#39: 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
#43: 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
#44: 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 ... , 9 types, 9 molecules npt0AAACAJAMAO

#8: 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
#10: 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
#14: 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
#21: 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
#28: 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
#30: 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
#37: 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
#40: 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
#42: Protein/peptide 60S ribosomal protein eL41


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

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

#16: 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
#20: 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
#38: 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

#41: 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
#45: 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
#78: 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
#79: 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

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

#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: O42817
#48: 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
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / 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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PL99
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5AJ93
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q59T44
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ADQ6
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PCG7
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q96W54
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5A7K0
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PNQ6
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: Q5ALV6
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PTI7
#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 SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / References: UniProt: A0A1D8PSK2

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

#49: 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
#50: 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
#52: 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
#56: 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
#57: 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
#58: 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
#60: 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
#61: 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
#62: 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
#63: 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
#64: 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
#65: 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
#66: 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
#67: 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
#70: 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
#75: 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
#76: 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

-
Non-polymers , 3 types, 10 molecules

#80: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#81: 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: obtained synthetically / Formula: C15H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Candida albicans 80S ribosome / Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL
Molecular weightValue: 3.3 MDa / Experimental value: NO
Source (natural)Organism: Candida albicans SC5314 (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

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

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180636 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more