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- PDB-7q08: Structure of Candida albicans 80S ribosome in complex with cycloh... -
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Basic information
Entry | Database: PDB / ID: 7q08 | ||||||||||||||||||
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Title | Structure of Candida albicans 80S ribosome in complex with cycloheximide | ||||||||||||||||||
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![]() | RIBOSOME / Candida albicans / cycloheximide / drug design | ||||||||||||||||||
Function / homology | ![]() 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 / yeast-form cell wall / filamentous growth of a population of unicellular organisms in response to starvation / GCN2-mediated signaling / regulation of cytoplasmic translation / hyphal cell wall ...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 / yeast-form cell wall / filamentous growth of a population of unicellular organisms in response to starvation / GCN2-mediated signaling / regulation of cytoplasmic translation / hyphal cell wall / fungal biofilm matrix / 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 / 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 / translation regulator activity / positive regulation of autophagy / ribosomal small subunit export from nucleus / 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 / cellular response to starvation / rescue of stalled ribosome / 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) / 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 / extracellular vesicle / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / cell adhesion / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / 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 / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å | ||||||||||||||||||
![]() | Zgadzay, Y. / Kolosova, O. / Stetsenko, A. / Jenner, L. / Guskov, A. / Yusupova, G. / Yusupov, M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 13741MC ![]() 7pzyC ![]() 7q0fC ![]() 7q0pC ![]() 7q0rC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 4 types, 4 molecules 134A
#1: RNA chain | Mass: 1085306.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 38943.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 50683.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: RNA chain | Mass: 575838.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Ribosomal 60S subunit protein ... , 28 types, 28 molecules jklmoqrsuwxy256789ABADAEAFAGAHAIALAPAQ
-60S ribosomal protein ... , 9 types, 9 molecules npt0AAACAJAMAO
#8: Protein | Mass: 19798.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#10: Protein | Mass: 28549.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 23105.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 20376.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 15551.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#30: Protein | Mass: 7135.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 11096.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 6347.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein/peptide | Mass: 3396.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal protein ... , 3 types, 3 molecules vzAK
#16: Protein | Mass: 24389.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#20: Protein | Mass: 21942.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 10102.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 4 types, 4 molecules ANigh
#41: Protein | Mass: 6078.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#45: Protein | Mass: 29126.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#78: Protein | Mass: 22615.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#79: Protein | Mass: 34593.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-40S ribosomal protein ... , 14 types, 14 molecules BCFHIJNWXZabcf
#47: Protein | Mass: 28759.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#48: Protein | Mass: 29041.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 29435.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#53: Protein | Mass: 27146.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 21285.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: Protein | Mass: 22801.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#59: Protein | Mass: 15715.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#68: Protein | Mass: 9652.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#69: Protein | Mass: 14807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#71: Protein | Mass: 15546.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#72: Protein | Mass: 11633.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#73: Protein | Mass: 13606.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#74: Protein | Mass: 8982.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#77: Protein | Mass: 7127.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal 40S subunit protein ... , 17 types, 17 molecules DEGKLMOPQRSTUVYde
#49: Protein | Mass: 26917.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#50: Protein | Mass: 27313.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: Protein | Mass: 25319.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 21765.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#57: Protein | Mass: 13836.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 17638.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 16976.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#61: Protein | Mass: 14052.112 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#62: Protein | Mass: 15967.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#63: Protein | Mass: 15769.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#64: Protein | Mass: 15770.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#65: Protein | Mass: 17023.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#66: Protein | Mass: 16097.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#67: Protein | Mass: 13366.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#70: Protein | Mass: 16000.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#75: Protein | Mass: 7536.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#76: Protein | Mass: 6615.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 10 molecules ![](data/chem/img/SPD.gif)
![](data/chem/img/3HE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/3HE.gif)
![](data/chem/img/ZN.gif)
#80: Chemical | ChemComp-SPD / |
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#81: Chemical | ChemComp-3HE / |
#82: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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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-#79 / Source: NATURAL |
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Molecular weight | Value: 3.3 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
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 |
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3D reconstruction | Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180636 / Symmetry type: POINT |